With the rise of the Qing Dynasty (1644–1911) a tension between Muslims and the government arose which eventually led to uprisings of Muslims against the regime and drastically reduced the numbers of Muslims. The Qing Dynasty was established by Manzu, a minority from northeast China. As a strategy of governance, the rulers tried to evoke the enmity among different ethnic groups by imposing policies of discrimination. This led to several bloody Hui-Hui uprisings during last half of 19th century in Gansu, Yunnan, Shanxi and Ningxia province, causing the death of millions of lives.
Among these uprisings, the most influential is that of Du Wenxiu (1856–1873) in Yunnan province. A rebel army successfully captured the city of Dali and rendered it the base for operations. Later they declared a separate kingdom from the Manzu government and named their state Pingnan Guo (平南国 The Pacified Southern Kingdom). The kingdom lasted 18 years, but it was eventually overthrown by the Manzu government troops with a loss of millions of Muslim lives, including Du Wenxiu himself. Another influential uprising was that of Shanxi Muslims which was caused by Qing officials’ the suppression and discrimination towards Muslims in Shanxi province. The uprising occurred at Shenxi province in 1862, but the flames of war spread all over northwestern areas e.g. Ningxia, Gansu, Qinghai and Xinjiang, continuing for over 15 years (1862–1877). It was put down by expelling the last resistant force led by Bai Yanhu(1840 -1882) from China to Russia. The uprising resulted in a huge number of casualties of Muslim lives and the complete elimination of Muslim influence on Shanxi province except for a small community in Xi'an, the capital of Shanxi.
Muslims in the Qing Dynasty generally fell under suppression by Manzu rulers under a policy of genocide long advocated by officials in the Manchu government. Some Muslims were compelled to hide their religious identity after escaping and were later assimilated by the Chinese. In spite of the persecution and discrimination suffered at the hands of the government, Muslims in Islamic learning and research achieved a tremendous progress during this period. Outstanding scholars continued appearing in public and made contributions to the spread of Islam in China and as well as enriched Chinese culture. Personalities such as Wu Zunqi (1598-1698), Mu Zhu (1640-1711), Liu Zhi (1655-1745), Ma Dexin (1794－1874), and Ma Lianyuan (1841--1895), have been so influential that their works are still read by wide range of the people today and laying the foundations for Islamic research in China.