The Shenzhou 9 capsule completed the maneuver with the Tiangong 1 module shortly before 1 p.m. (0500 GMT). The docking was shown live on national television. It follows a docking last week that was carried out by remote control from a ground base in China.
The Chinese astronauts have been living and working in the module for the past week as part of preparations for manning a permanent space station. They returned to the Shenzhou 9 capsule early Sunday and disconnected in preparation for the manual re-connection.
The crew includes 33-year-old Liu Yang, an air force pilot and China's first female space traveler.
Liu is joined by mission commander and veteran astronaut Jing Haipeng, 45, and crew mate Liu Wang, 43.
Their mission, which is expected to last at least 10 days, is China's fourth manned mission. Shenzhou 9 launched June 16 from the Jiuquan center on the edge of the Gobi desert in northern China.
China is hoping to join the United States and Russia as the only countries to send independently maintained space stations into orbit. It is already one of just three nations to have launched manned spacecraft on their own.
Another manned mission to the module is planned later this year.
The Tiangong 1, which was launched last year, is due to be replaced by a permanent space station around 2020. That station is to weigh about 60 tons, slightly smaller than NASA's Skylab of the 1970s and about one-sixth the size of the 16-nation International Space Station.