The Manchus conquered Inner and Outer Mongolia, incorporating them into their empire. The Manchu emperor became the sovereign of Mongolia. Nevertheless, the majority of Mongol nobles retained their titles. The Qing government reorganized the administration of Inner Mongolia with their consent.

The 24 provinces of Inner Mongolia were divided into 6 regions. The Qing empire appointed a governor for Outer Mongolia who resided in the city of Uliastai. There was also another administration in the city of Ih Huree that managed Inner Mongolia. When western Mongolia finally succumbed to the Manchus, they established the Khovd government in 1725. The Manchu government formed four provinces, the province of Khan Sain in tribute to his contribution in the war against the Oirats.

When the Mongols converted to Buddhism in 1639, they elected a superior to lead the Buddhist Church under the title of Bogd. The Bogd was responsible for religious affairs and when the Manchus arrived, they retained him as the official Buddhist leader. A special ministry controlled the acts of the Bogd and Buddhist ceremonies. Thus the Qing empire created an extremely elaborate administration, with taxes and political arrangements for Inner and Outer Mongolia.

The Mongols resisted Manchu imperialism through rebellions and mutinies. In 1755, a great number of Mongols launched an attack that encircled western Mongolia. Among the rebels were the boshigt Galdan, Amarsanaa and Chingunjav. The attack was initially successful but the Manchus gained the upper hand and severely punished the mutineers. Amarsanaa fled Mongolia and found refuge in Russia where he died. The others were executed.

Manchu laws in Mongolia covered all aspects of Mongol life. "Halh Juram," which was passed between 1709 and 1795, was the legal document of this era. There was also "the legal writings of Inner Mongolia," which were established in 1817. This consisted of 63 volumes of various legal cases.

During the period of Manchu domination, Mongol literature experienced a renaissance. Poets and writers produced remarkable religious and secular works. The most famous was the monk Danzanrawjaa who lived in the 19th century and was a great dramatist. His best-known work was "Saran höhöö."

The Manchu government stifled any idea of autonomy in Mongolia. Consequently, Mongolia spent the 19th century as a minor region of the Qing empire.