For the first time, whole auto-pilot near the 7000 meters bottom was accomplished in the manned deep submersible “Jiaolong”. Its whole control system was deeply researched. In order to overcome its wild measuments, especially the steps between the control period and measuments period, variable dimension adaptive unscented Kalman filter is adopted for the precise navigation. Control strategy makes use of fuzzy theory for the purpose of control parameter automatic changing on-line, and number theory based experiment data processing method. Five automatic control functions were reached for its motion, including automatic heading, depth, altitude, velocity and dynamic positioning. Under complicated ocean environment, its precise navigation, control, information interface in cabin, surface information console, black-box data analysis, and semi-physical digital simulation technology was researched. The sea trial experiments during August to October 2009, May to July 2010, July to August 2011, and June to July 2012 showed that the control system can satisfy its demand, and it is advanced, reliable and good control performance.