The quake, measuring 3.2 on the Richter scale, was felt across Zigui County, China's official Xinhua news agency reported.
Three Gorges is the world's largest water control and hydropower project. It spans the Yangtze River, China's longest waterway.
"The minor earthquake has not affected the Three Gorges Dam, which can endure far stronger earthquakes," said a spokeswoman for the China Three Gorges Corp.
She said no earthquake-triggered landslides have been reported in the reservoir area and all power-generating units are working normally.
There were no immediate reports of casualties.
"Wednesday's earthquake was a shallow-focus earthquake rather than a structural one," said Zhang Shuguang, the head of the water project's management bureau.