As empress, Empress Zhangsun was said to be frugal and humble, taking only the supplies that she needed without living luxuriously. When Crown Prince Chengqian's wet nurse the Lady Sui'an stated that his palace lacked sufficient goods and requested more, she replied, "All a crown prince should worry about is not having enough virtues or enough fame. Why worry about not having enough goods?" It was also said that she rarely got angry with the ladies in waiting and eunuchs who served her. She often gave Emperor Taizong examples from history to inspire him to rule better. At times, if Emperor Taizong got angry at the ladies in waiting or eunuchs for no reason, she would pretend to be angry as well and ask to personally interrogate them and hold them in custody; she would then wait until his anger had subsided, and then begin to plead on their behalf, thus reducing improper punishments within the palace. It was said that whenever Emperor Taizong's concubines or ladies in waiting would be ill, she would personally visit them and reduce her own expenditures to treat them.

Emperor Taizong would at times try to discuss with her matters of award and punishment to see what she opined, but each time she refused to do so, stating that it was not her place to do so. As her brother Zhangsun Wuji was a major strategist who contributed much to his victory over Li Jiancheng, he wanted to make Zhangsun Wuji a chancellor, and Empress Zhangsun declined on Zhangsun Wuji's behalf, stating:

"I have the opportunity to be here in the palace, reaching the highest of honors. I do not wish to see my brothers and nephews wield power. What happened to the households of Han Dynasty's Empress Lü Zhi and Huo Guang are cruel examples of what might happen. I pray that Your Imperial Majesty will not make my brother chancellor. "

Emperor Taizong initially disagreed and made Zhangsun Wuji chancellor anyway in fall 627, but with Zhangsun Wuji himself also repeatedly declining, Emperor Taizong relented in spring 628 and removed Zhangsun Wuji from the chancellor position.

Also in 627, Empress Zhangsun's other brother Zhangsun Anye was implicated in a treasonous plot, along with the generals Li Xiaochang (李孝常), Liu Deyu (刘德裕), and Yuan Hongshan (元弘善). Initially, Zhangsun Anye, like the other conspirators, were to be put to death, but Empress Zhangsun interceded on his behalf, stating that even though Zhangsun Anye deserved death, the people would have thought that she was retaliating for his ill treatment of her and Zhangsun Wuji when they were little. Emperor Taizong agreed and spared Zhangsun Anye, only exiling him to Xi Prefecture (roughly modern Liangshan Yi Autonomous Prefecture, Sichuan).

In 632, Emperor Taizong was about to marry the Princess Changle to Zhangsun Wuji's son Zhangsun Chong (长孙沖). As the princess was born of Empress Zhangsun and was his favorite daughter, Emperor Taizong ordered that her dowry had to exceed that for his sister, the Princess Yongjia. The chancellor Wei Zheng advised against it, pointing out that this was contrary to Emperor Ming of Han's observation that his sons should not be as honored as his brothers. Emperor Taizong agreed and also informed Empress Zhangsun, who was greatly impressed with Wei's honest advice, and therefore, after receiving permission from Emperor Taizong, she had her eunuchs send rewards of money and silk to Wei, praising him for his honesty. On another occasion, after Emperor Taizong returned from an imperial gathering, he was angry and yelled, "Let me find a chance to kill this red-neck!" Empress Zhangsun asked whom he was referring to, and he replied, "I am referring to Wei Zheng. He always find a way to insult me in front of everyone in the imperial hall!" Empress Zhangsun retreated to her bedchambers and put on the official empress gown; standing solemnly, she prepared to bow to Emperor Taizong. He was surprised, and asked her what the reason was. She responded, "I have heard that only a most able emperor will have subordinates who have integrity. Wei shows this much integrity because you are an able emperor. How can I not congratulate you?" Emperor Taizong's anger turned to happiness, and he did not punish Wei. Later that year, on an occasion when Emperor Taizong and she personally visited Emperor Gaozu (who had then taken the title of Taishang Huang (retired emperor)) at his Da'an Palace (大安宫), they personally served a feast to him.

Emperor Taizong, for several years, had often suffered from severe illnesses, and Empress Zhangsun often attended to him day and night, carrying poison within her belt and resolving to commit suicide if the emperor should die. Empress Zhangsun herself was said to suffer from severe asthma, and her conditions were exacerbated in 634 when she was ill, but nevertheless attended to Emperor Taizong when he was forced to wake up in the middle of the night and put on armor and weapons due to an emergency report by his brother-in-law, Chai Shao (柴绍) the Duke of Qiao. By 636, her conditions were severe, and Li Chengqian suggested to her that, as the doctors appeared to have done everything they could, Emperor Taizong declare a general pardon and encourage commoners to become Buddhist or Taoist monks, to try to gain divine favor. Empress Zhangsun, knowing that Emperor Taizong had long disapproved of Buddhism and Taoism and herself believing over use of pardons to be improper, refused. Li Chengqian instead told the idea to the chancellor Fang Xuanling, who reported it to Emperor Taizong. Emperor Taizong considered issuing a general pardon, but Empress Zhangsun again refused. As she came close to death (at a time that Fang had drawn anger from Emperor Taizong and was temporarily relieved of his post and returned to his mansion), she bid Emperor Taizong goodbye with these words;

"Fang Xuanling had served Your Imperial Majesty for a long time. He is careful, and all of his wonderful strategies and secret plans were not revealed to anyone. Unless there is a particularly good reason, I hope that you will not abandon him. As to my Zhangsun clan, many of them enjoy high salaries and high positions on account of our marriage, not because of their great virtues, and therefore they can crumble easily. In order to preserve the Zhangsuns, I hope that you will not put them in powerful positions, and that they would be satisfied with seeing you at imperial gatherings the first and 15th day of each month. During my lifetime, I made no contributions to the people, and I should not harm them in my death. I hope that you will not build a tomb to cause the people to labor and the empire to waste resources. Make a hill my tomb, and only use brick or wooden implements in the tomb. I hope that Your Imperial Majesty will continue to be close to honest men and stay away from those lacking virtues; that you will accept faithful words and reject wicked flattery; that you will decrease labor and stop hunting. Even as I go into the underworld, if these things happen, I will have no regrets. It is not necessary to summon the sons and daughters back here; if I see them mourn and cry, I will only be saddened."

She died in 636. After she died, the palace authorities submitted Empress Zhangsun's writings -- a 30-volume work titled Examples for Women (女则, Nü Ze), and a commentary criticizing Han Dynasty's Empress Ma -- to Emperor Taizong. When Emperor Taizong read her works, he was greatly saddened, and he stated:

"This book, written by the empress, is capable of being an example to generations. It is not that I do not know the will of heaven and mourn uselessly, but now, when I enter the palace, I can no longer hear her corrective words. I have lost a wonderful help, and I cannot forget her."

He summoned Fang back to his chancellor position, and then he buried her with honors due an empress, but reduced the expenditures to the extent possible, as she wished. He himself would eventually be buried at the same tomb, after his death in 649.