The constituent parts and control principle of digit servo tracking system were introduced in this paper, and several factor which may influence the selection of the micro controller were also discussed. The management software module of the servo tracking system, the servo control algorithm module of strap down inertial/GPS unit and the servo control test software module were investigated based on the system task classification and the software modularization. The designed software was loaded in the micro controller to testify the servo tracking system. The result indicated that the software design of the servo tracking system had good performance with high value of engineering application.