The mechanism of analog distortion TMB fault in the circuit fault of the satellite navigation system is theoretically analyzed and simulated. In addition, the correlation function and power spectrum of pseudo code are analyzed. Based on the characteristics of Field-Programmable Gate Array (FPGA) and modulation mode, the design method of quantization after oscillation of the pseudo code is proposed. The paper focuses on its implementation on FPGA and analyzes the key technology of IIR filter. Then the correlation function of the fault signal and its influence on the positioning result are tested through the fault injection which is realized based on the self-research satellite navigation system simulator platform. The test results show that the larger the oscillation frequency and attenuation coefficient in the design system, the smaller the impact on the positioning of the system.