The warship is generally equipped with photoelectric theodolite in carrier-borne aircraft flying test. Due to the low frequency of guidance source signal and disturbance from environment, the performance of the system is restricted. We proposed an extrapolation-interpolation method and a three points cut-off method to solve the problem,respectively. To smooth the switch of different guidance sources, we also recommended a gradually tracking algorithm.All the methods above resolve data filter, interpolation and multi-source problem effectively, which are usually encountered in the guiding photoelectric theodolite on the shipboard. At last, the guidance formulae of moving platform are established based on GPS/INS navigation information.