An on-board computer system should have such advantages as light weight, small volume and low power to meet the demand of micro-satellites. This paper, based on specific characteristics of Stereo Mapping Micro-Satellite ( SMMS), describes the on-board computer system with its advantage of having centralized and distributed control in the same system and analyzes its reliability based on a Markov model in order to provide a theoretical foundation for a reliable design. The on-board computer system has been put into use in principle prototype model of Stereo Mapping Micro-Satellite and has already been debugged. All indexes meet the requirements of the design.