Comprehensive system error estimation on mobile platform sensor registration is a difficult problem.In order to estimate the comprehensive system error for the mobile platform of shipsthis paper presents two methods using the highprecision GPS information obtained through cooperative target.In the first methodan observation model was built up to decouple error component in equivalent error model based on itand the approximate equivalent value was used to estimate each component of comprehensive system error.The first method can overcome the shortage of equivalent error model.In the second methodthrough analyzing the effect of error component on the location precision and linearizing the influence functionthe observation function was established and estimation of comprehensive system error was implemented.Simulation is made for two situationsand the simulation results demonstrate that each method has its advantages and disadvantages.On the wholethe performance of the second method is better.The position precision is improved greatly after error correction using the estimation results of these methods.