For the suppression of linear frequency modulation interference in a direct sequence spread spectrum system,a new method is proposed based on the Short Time Fourier Transform(STFT) and the Fractional Fourier Transform(FRFT). At first, the parameters of the linear frequency modulation interference is estimated coarsely using STFT, then the fine search for correct parameters is implemented in FRFT. At last, according to the position and intensity of the pulse by linear frequency modulation interference in the Fractional Fourier domain, it is adaptive to choose the field to Sachieve the purpose of the suppression of linear frequency modulation interference. Simulation results show that the proposed method works well to suppress the linear frequency modulation interference and the performance of bit error rate (BER) can improve more than 1000 times when jammer to signal ratio(JSR)<40