In weak GNSS signal environments, due to navigation data bit, the dynamic of receiver and the quality of receiver’s oscillator, the traditional carrier loop cannot use long coherent integration time to enhance input SNR of the loop. A navigation data bits estimation method based on FFT is proposed, which just needs to calculate the FFT of one combination of data bits’ signs. The FFT of the received signal under any other data bits combination can be obtained through a few additions. The proposed method reduces the calculation complexity of navigation data bits’ signs estimation. Based on the estimation of the signs and bit edges of navigation data bits, the proposed method can adopt short coherent integration time samples over long time and FFT to discriminate doppler frequency error, which can overcome the SNR degradation introduced by receiver’s dynamic and doppler frequency estimation error over long coherent integration time and enhance the output SNR of the loop. Simulation results show that the proposed carrier tracking method can track carrier frequency in weak signal and low dynamic environments.