State media reports gave no immediate reason for removing Wang Lequan, 65, who had served as party boss in Xinjiang since 1995.
He was replaced by Zhang Chunxian, who turns 57 next month and has been the party boss in southern Hunan province since November 2006.
The official Xinhua News Agency said the change was announced by the Central Committee of the Communist Party of China. It said Wang had been appointed as the deputy secretary of a political committee of the Central Committee. It is not known if he is still a member of the party's Politburo, the 25-member body near the pinnacle of power in China.
Wang was in charge last July when bloody street riots in the regional capital of Urumqi pitted minority Uighurs (pronounced WEE-gers) against ethnic majority Han Chinese. Almost 200 people were killed, mostly Han, in the country's worst communal violence in decades.
The Uighurs see Xinjiang as their homeland and resent the Han Chinese who have moved into the region in recent decades. A simmering separatist campaign has occasionally boiled over into violence in the past 20 years.
Overseas Uighur activist Dilxat Raxit said the change in leaders was not enough. He said Uighurs needto be given more political rights and input into decision making.
"China must make fundamental changes in the way of ruling through suppression in Xinjiang and respect the political demands of the Uighur people," said Raxit, spokesman for the Germany-based World Uyghur Congress.
The government says it has poured billions of dollars into the area and substantially raised living standards.