She oversaw the emperor's education while the Grand Secretary Zhang Juzheng and the highest-ranking eunuch of the imperial palace, Feng Bao, managed the state administration.

Although she did not typically involve herself in politics, she did intervene in the dispute over the appointment of the heir to the throne, where she supported the rights of the emperor's eldest son.

Lady Li was granted the title of empress dowager and, as per the law, assumed the role of head of government during her son's minority.

She formed an alliance with Senior Grand Secretary Zhang Juzheng and the highest-ranking eunuch in the imperial palace, Feng Bao.

Together, they ruled the empire, with Zhang overseeing the government, Feng Bao managing the imperial eunuchs, and Lady Li supervising the Wanli Emperor's education.

[a] The Wanli Emperor's deep respect and devotion towards his mother, instilled by his strict upbringing, prevented him from openly opposing her throughout his life.

However, in the mid-1590s, a disagreement with the emperor over the appointment of an heir to the throne caused a rift, resulting in her having fewer resources to fund projects.

[8] In 1586, the issue of succession arose when the emperor's favored concubine, Lady Zheng, gave birth to a son, Zhu Changxun (1586–1641).

The emperor had agreed to begin the education of his eldest son in early 1594, but this concession was followed by attacks on the empress dowager.

The following year, he demoted and transferred a high-ranking and respected eunuch, Zhang Cheng (張誠), who was related to Lady Li's family, to Nanjing.

In 1600, the emperor bestowed a high honorary title on the Taoist Geng Yilan, who had participated in the arrest of Hanshan Deqing.

Their relationship continued to be steadily good as the Wanli Emperor ceased the persecution of Buddhists, which he had previously attacked in the decade prior.

As a result, the empress mother returned to public life on a larger scale after 1604, renewing her support for Buddhist institutions that had been subdued in the decade after 1594.