In 706, his younger brother Emperor Zhongzong provided Li Xian with an honorable burial by interring his remains at the Qianling Mausoleum.

Emperor Gaozong soon ordered that much of government matters be ruled on by Li Xian, But because most of the imperial work was done by Empress Wu, his decisions were under her mother's control.

Also around this time, Li Xian led a group of scholars, including Zhang Da'an, Liu Nayan (劉訥言), Ge Xiyuan (格希元), Xu Shuya (許叔牙), Cheng Xuanyi (成玄一), Shi Cangzhu (史藏諸), and Zhou Baoning (周寶寧), in writing commentaries for the Book of Later Han, the official history of the Eastern Han dynasty, written by the Liu Song scholar Fan Ye.

Empress Wu, detecting this, had her literary staff write two works entitled, Good Examples for Shaoyang (少陽正範, "Shaoyang" being an oblique term for a crown prince) and Biographies of Filial Sons (孝子傳) and gave them to Li Xian, and further wrote a number of letters rebuking Li Xian, making him more fearful.

At the same time, Empress Wu relieved his duties as head of many government decisions and changed all of Li Xian's previous policies.

(Some historians, pointing to oblique references that he was "particularly close" to a number of male servants, also believe that he liked sexual relations with both women and men.)

When Empress Wu heard this, she had people report the news to Emperor Gaozong, who then ordered an investigation, led by the officials Xue Yuanchao, Pei Yan, and Gao Zhizhou.

In spring 684, she sent the general Qiu Shenji to Ba Prefecture with the order of, "Examine the house of Li Xian the former crown prince to prevent external attacks."

When news of Li Xian's death arrived at Luoyang, Empress Wu publicly blamed Qiu and demoted him to the post of prefect of Die Prefecture (疊州, roughly modern Gannan Tibetan Autonomous Prefecture, Gansu), while publicly mourning Li Xian and posthumously creating him the title of Prince of Yong.