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In this paper, the representation of Doppler effect on code acquisition performance is analyzed and the principle of combining serial-parallel correlator with FFT is given based on the discrete-time signal processing. The improved code acquisition architecture by combining twi-serial-parallel correlator with FFT for the long PN code spread spectrum communication system is designed and realized in FPGA and DSP. This architecture provides a very good trade-off between acquisition performance and complexity. Application results show this architecture is very attractive for the long PN code spread spectrum communication system.