In high dynamic and weak GNSS signal environments, long coherent integration is necessary to enhance the acquisition sensitivity. High dynamic results in large Doppler frequency range, and long integration time results in small Doppler frequency bin. The above two reasons induce high calculation complexity. To improve the flexibility of acquisition process, twostage FFT acquisition method is presented in this paper. The first stage FFT performs upon received signal across short time, which divides the Doppler frequency range into multiple coarse sub-ranges. The second stage FFT is executed on the output of the first stage FFT, and estimates fine Doppler frequency in every coarse Doppler frequency sub-range. To maintain phase continuous, phase compensation needs to perform on the output of the first stage FFT. Simulation results show that the presented two-stage FFT acquisition method can acquire weak GNSS signals with large Doppler frequency range.