Lady Borjigit was born on the third day of the tenth lunar month in the 16th year of the reign of Hong Taiji, which translates to 5 November 1641 in the Gregorian calendar.

On 25 October 1653, the Shunzhi Emperor deposed his first empress consort, Erdeni Bumba, who was also from the Borjigit clan.

In June or July 1654, Altantsetseg entered the Forbidden City and became a concubine of the Shunzhi Emperor.

In July or August 1654, she was officially designated as the empress to replace the deposed Erdeni Bumba.

The Shunzhi Emperor died on 5 February 1661 and was succeeded by his third son, Xuanye, who was born to Lady Tunggiya.