The earthquake hit Baicheng county in the northwestern Aksu prefecture at 5.14 am, according to the China Earthquake Networks Center.
Footage showed buildings swaying in the dark, leaving some houses with their roofs caved in afterward.
"The earthquake caused three deaths and 65 houses were damaged," state broadcaster CCTV reported, adding that there were 10 aftershocks of which the largest magnitude was 3.4.
After houses and livestock sheds collapsed, leaders of an affected village set up a temporary resettlement site.
China is regularly hit by earthquakes, especially in its mountainous western and southwestern regions.
In February 2003, a powerful 6.8-magnitude quake killed 268 people in Xinjiang and caused significant damage.
Following Wednesday's earthquake, train services between regional capital Urumqi and areas such as Hotan and Aksu were delayed, the official Xinhua news agency reported.
A powerful 7.9-magnitude quake in southwest China's Sichuan province in 2008 left 87,000 people dead or missing.
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