Images of the capsule landing in Inner Mongolia at 10:05 local time (02:05 GMT) were shown live on television.
The astronauts, including China's first woman in space, carried out a successful manual docking with the Tiangong-1 laboratory module.
The mission is a key step towards China's goal of building a space station by 2020.
Premier Wen Jiabao hailed the mission as a "complete success".
By Jonathan AmosScience correspondent
The smiles said it all. Jing Haipeng, commander of the Shenzhou-9 crew, was the first to emerge from the return capsule, followed by his flight engineers Liu Wang and the country's first woman astronaut, Liu Yang.
The Shenzhou-9 mission posted a series of firsts: the first manned automatic and manual dockings; the first long-duration spaceflight; and the first crew to live aboard a permanently orbiting module, Tiangong-1.
Beijing has long talked about its three-step strategy.
The first step was the development of the Shenzhou capsule system itself, the second involved the technologies needed for spacewalking and docking, and the third is China's own space station.
But a word of caution. Spaceflight, to quote the old cliche, is hard, and at some point the Chinese programme will encounter problems.
The history of spaceflight tells us unfortunately that some adversity is inevitable. It will be interesting then to see how the Beijing authorities react.
Jonathan Amos' full analysis
"This is another outstanding contribution by the Chinese people to humanity's efforts to explore and use space," Mr Wen said in Beijing.
"It feels so good to stand on Earth, and it feels even better to be home," astronaut Liu Wang was quoted by national broadcaster CCTV as saying.
"Tiangong-1, our home in space, was comfortable and pleasant. We're very proud of our nation," female astronaut Liu Yang said.
The crew of the Shenzhou-9 craft successfully carried out the country's manual docking manoeuvre earlier in the week.
The delicate procedure, which involved bringing together two orbiting vessels travelling at thousands of miles an hour, was mastered by the USSR and US space teams in the 1960s.
The crew also carried out automatic docking of the two crafts during their mission.
The three astronauts returned to the Shenzhou-9 spacecraft on Thursday and performed a manual separation from the space laboratory.
They touched down in Inner Mongolia's Siziwang county, with the capsule deploying a parachute to slow its approach.
All the astronauts were in good health, state-run news agency Xinhua reported. They were shown on CCTV leaving the capsule carried on chairs, smiling as they waved to supporters.
The crew included Jing Haipeng, 45, the mission commander and a veteran astronaut, Liu Yang, 33, and Liu Wang, 43, who performed the manual docking.
Ms Liu, 33, is a major in China's air force from the central province of Henan. On China's Tencent QQ messaging service, she goes by the name "little Flying Knight".
She was recruited into China's space programme only two years ago, but she excelled, the official news agency Xinhua says.
The Shenzhou-9 spacecraft was launched on 16 June.
A Chinese space capsule carrying three crew members has returned to Earth following a 13-day mission.