Abstract: In this paper, a frequency domain interference estimation and time domain cancellation method is proposed to suppress the time-varying single tone jamming (STJ) in direct sequence spread spectrum (DSSS) system. The interference channel is modeled as a time-varying fading channel in the system. In this method, the parameters of time-varying STJ are estimated in frequency domain, and then it is reconstructed and subtracted from the raw data. Furthermore, the BER expression is analyzed to assess the performance of the proposed method. Simulation results demonstrate the effectiveness of the method in mitigating time-varying STJ and approaching the interference-free performance limit over practical ranges of STJ power levels and mobility levels. In the frequency selective fading channel, when signal-to-noise ratio (SNR) is 20 dB, the spreading gain is 16, Doppler shift of the interference channel is 100 Hz, jamming-to-signal power ratio (JSR) is less than 20 dB, the STJ can be suppressed by the proposed method.