The invention discloses a CDMA communication anti-interference system based on frequency domain filtering. The CDMA communication anti-interference system comprises a signal preprocessing portion, a frequency domain processing portion and a post-processing portion, wherein the signal preprocessing portion comprises an A/D collector, a digital down-converter, a low-pass filter and an extractor which are connected in sequence; the frequency domain processing portion comprises two routes, one route comprises a windowing device, an FFT device, a threshold value generating and spectral line processing device, an IFFT device and 50% delay device which are connected in sequence, the other route comprises a 50% delay device, a windowing device, an FFT device, a threshold value generating and spectral line processing device and an IFFT device which are connected in sequence, and finally, the two routes are connected with an adding device simultaneously; the post-processing portion comprises an interpolation device, a filter, a digital up-converter and a D/A converter which are connected in sequence. The invention further discloses a CDMA communication anti-interference method based on frequency domain filtering. By means of the system and the method, the anti-interference ability of the system is effectively enhanced.