The astronauts were on a six-month rotation at the space station and originally scheduled to return on November 5, four days after the new crew arrived.
Their return was delayed for more than a week.
Their capsule was expected to land in a remote part of northwest China's Inner Mongolia region on Friday.
China's Manned Space Engineering Office said there were minor cracks in a window of the return capsule of the Shenzhou-20 spacecraft, most likely caused by impact from space debris.
There are millions of pieces of mostly tiny debris circling the earth at speeds faster than a bullet flies.
They can come from launches and collisions and pose a risk to satellites, space stations and the astronauts who operate outside them.
The three Chinese astronauts — Chen Dong, Chen Zhongrui and Wang Jie — were coming back on the Shenzhou-21 craft, the Manned Space Engineering office said.
The Shenzhou-20 will remain in orbit, it said.
The crew, which had travelled to the Tiangong space station in April, was "in good condition, working and living normally," the engineering office said earlier this week.
China's space program has made steady progress since 2003.
It has built its own space station and has a goal of landing a person on the moon by 2030.
The latest Shenzhou-21 mission brought four mice to the space station to study how they would be affected by weightlessness and confinement.
