The Yuanwang-3 tracking ship off the coast of Namibia picked up the spacecraft's signal at 18:49 UT, and commanded retro-fire. This time the spacecraft accepted the command, which probably saved the entire program. The spacecraft passed out of range of the tracking ship nine minutes later. Its trajectory arced over Africa, skimmed the coast of the Arabian peninsula, and then over Pakistan, before re-entering over Tibet.
Following re-entry, the drogue chute deployed at an altitude of 30 km with the capsules soft-landing rockets firing 1.5 m above the ground. The capsule landed at 41 deg N, 105 deg E, (415 km East of its launch pad and 110 km north-west of Wuhai, Inner Mongolia), at November 20 19:41 UT. The spacecraft had completed 14 orbits of the earth in 21 hours and 11 minutes.
After the flight it was reported that not a single primary spacecraft system had failed, so none of the back-up systems were tested. The touchdown point was only 12 km from the predicted position. The soft landing braking rocket worked well - no damage was found to the capsule structure, heat shield or the seals. The jettisoned heat shield, parachute hatch, and drogue chute were found within 5 km of the landing point. The orbital module, which separated prior to retro-fire, continued in controlled flight until 27 November, when it decayed and reentered the atmosphere. A primary payload returned by Shenzhou were 100 kg of seeds, considered valuable to the Chinese after one day of exposure to the space environment. The Chinese space tracking fleet returned from the Shenzhou mission between 12 December 1999 and 4 January 2000. During their 259-day voyage, the four ships traveled 185,000 km and experienced some heavy seas while tracking and communicating with the Shenzhou for a total of 150 minutes.
The Communist Party of China Central Committee, the State Council and the Central Military Commission sent a congratulatory telegram after the flight to the departments and personnel involved. Three days after landing the capsule arrived, still sealed, at Beijing Aerospace City. Premier Jiang Zemin was personally present for the opening of the hatch, accompanied by leading figures in the program. The potential military applications of the spacecraft were emphasised in Chinese press releases. Zemin was identified as being present in his role as Chairman of the Central Military Commission. Others present included Vice-President Hu Jintao, Zhang Wannian, Chi Haotian (all as Vice-chairmen of the Central Military Commission), Cao Gangchuan, Head of the People's Liberation Army General Armaments Department, Xu Fuxiang, the President of the China Space Technological Research Institute, and Qi Faren, identified as Chief Designer of the spacecraft.
Qi said "The spacecraft voyage is successful and the module returned accurately and safely. However, we shall conduct more studies on concrete technical data such as temperature and humidity recorded by the module. It will provide us with more data to manufacture the manned spacecraft".
The module's payload included a dummy astronaut, national flags, the flag of the Macao Special Administrative region, a banner with all the signatures of the scientists and engineers who participated in construction of the spacecraft, commemorative stamps and some experimental seeds.