The proton precession magnetometer (PPM) is a commonly used device to measure the varying magnetic field. Since the frequency of the PPM sensing free induction decay (FID) signal is proportional to the magnetic field, the signal-to-noise ratio (SNR) is always a critical issue that influences the measurement accuracy severely due to the external interferences such as harmonic noise and random noise. In this study, to boost the SNR of the FID signal, an effective filtering algorithm based on time-frequency peak filtering (TFPF) analyzed with pseudo-Wigner-Ville distribution (PWVD) is proposed. Through pre-treating the collected noisy FID signal with frequency modulation and instantaneous frequency estimation using the peak value of the time-frequency characterization, the embedded noise can be decorrelated and the relative pure FID signal can be detected regardless of the impact of varying noise levels. The superiority of the proposed synaptic noise reduction framework, namely, TFPF-PWVD, was found by comparing it with state-of-the-art approaches under the same conditions. The results illustrated that even though in a strong-noisy scenario, the proposed TFPF-PWVD based approach still achieved the best SNR for the yielded sensing FID and the minimum standard deviation for the observed magnetic field data, which can enhance the geomagnetic measuring performance of a PPM.