Abstract: To achieve higher acquisition accuracy while using FFT(fast Fourier transform)-based algorithm to acquire spread spectrum signal, integration across data bit transition boundaries is necessary. However, performance degradation due to data modulation must be eliminated. Two effects of baseband data shift on acquisition performance, amplitude attenuation and frequency offset of the detected signal in frequency domain, were analyzed. A method to solve this problem was given. This algorithm constructs a complex signal which is free from data modulation, and detects Doppler shift using this signal through FFT. Simulation in MATLAB and FPGA(field programmable gate array)-based implementation of this method was also described. The simulation and experiment results verify that, this method can overcome the problem caused by baseband data shift, and improve acquisition accuracy by one times compared with conventional method in the same predetection integration time.