To improve the imaging quality of a Fourier Telescopy(FT) and to implement the high-resolution imaging for moving targets, the data processing methods to inhibit the spectral leakage generated by the frequency shift error from an acousto-optic frequency shifter, the bias of an optical device and truncating signals were researched and how to calculate the signal frequency in real time was given. Firstly, an all phase spectrum analysis technology was used to process sampling signals of a static target and a search algorithm was taken to capture the maximum frequency value of each interferometric beam. Then, the actual frequencies of any two beams were calculated by an all phase time shift phase difference correcting spectrum method. Finally, the frequency deviation and demodulated target's Fourier information were obtained and the demodulation frequency of the non-whole point was estimated by the least square fitting. The results show that the Strehl ratio of reconstructed image by proposed method is increased by 3% as compared with that of traditional methods. Furthermore, the new method has a higher inhibiting ability for spectral leakage, better reconstructed image, and it can provide the reference for data processing of moving targets.