Abstract: In high dynamic and long-term integration condition, the code Doppler frequency will lead to code phase migration in PMF-FFT algorithm, which is not conducive to the DSSS signal acquisition. After in-depth study on this issue, the quantitative relationship among the code phase migration, integration losses and parameters estimated bias were derived and simulated. Based on PMF-FFT algorithm, a compensation method for code Doppler frequency was proposed, which used Keystone transform to correct code phase migration, so as to compensate the code Doppler frequency. Simulation results show that, on the condition of 37 dB/Hz CNR, 10 ms coherent integration interval and a fixed false alarm possibility of 10^-6, the new algorithm can effectively eliminate the code Doppler frequency and has a single detection possibility of 98%.