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Time service is the precondition of precise navigation in radio navigation system, the cesium atomic clock of high stability is used in this system as frequency reference and GPS time receiver is used. To solve the problem of system synchronize error caused by satellite movement, Doppler frequency shift, ionosphere refraction, etc. sliding window method and discrete wavelet method are introduced in this paper. The results of calculation indicate that discrete wavelet transform can decrease the error caused by GPS time receiver jitter effectively.