Abstract: Satellite navigation signals are susceptible to strong interference. The frequency domain interference suppression (FDIS) algorithm is one of the most useful anti-jamming algorithms. Although this method can achieve effective interference suppression, it will also cause distortion of the auto-correlation function (ACF) of satellite signal, which will degrade signal acquisition performance. In order to analyze the influence of the FDIS algorithm on the acquisition performance, the ACF model of the satellite signal after anti-jamming is established.The ACF parameters are also analyzed, such as signal-to-noise ratio loss, peak sidelobe ratio, and first sidelobe position. Additionally, the acquisition performance model after FDIS method is further established, and the acquisition probabilities under different acquisition strategies are compared. Theoretical analysis and numerical simulation results show that the signal-to-noise ratio of the ACF after FDIS method decreases, side lobes appear beside the main lobe, and the distortion parameters are closely related to the interference parameters. It also shows that the signal acquisition performance deteriorates after the FDIS method. The research results provide important model support for improving signal acquisition performance in interference scenarios.