Deep space exploration navigation requires high accuracy of the Doppler measurement, which is equivalent to a frequency estimation problem. Because of the fence effect and spectrum leakage, the frequency estimation performances, which is based on the FFT spectrum methods, are significantly affected by the signal frequency. In this paper, we propose a novel method that utilizes the mathematical relation of the three Chirp-Z Transform (CZT) coefficients around the peak spectral line. The realization, unbiased performance, and algorithm parameter setting rule of the proposed method are described and analyzed in detail. The Monte Carlo simulation results show that the proposed method has a better anti-noise and unbiased performance compared with some traditional estimator methods. Furthermore, the proposed method is utilized to process the raw data of MEX and Tianwen-1 satellites received by Chinese Deep Space Stations (CDSS). The results show that the Doppler estimation accuracy of MEX and Tianwen-1 are both about 3 millihertz (mHz) in 1-s integration, which is consistent with that of ESA/EVN/CDSN and a little better than that of the Chinese VLBI network (CVN). Generally, this proposed method can be effectively utilized to support Chinese future deep space navigation missions and radio science experiments.