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With the increasing competition in Global Navigation Satellite System(GNSS),the development of satellite navigation industry has become a big challenge for our country in recent years.Focusing on the development trend and effective demand of BeiDou system(BDs),a low complexity algorithm for code Doppler compensation using FFT-based parallel code searching architecture is proposed to correct Pseudo-Random Noise(PRN)code phase migration,which is caused by the code Doppler in the acquisition process of navigation signal in high dynamic and low Carrier-Power-to-Noise-Density Ratio(C/N0)environment.