Magnetic resonance sounding (MRS) has the advantage of detecting groundwater content directly without drilling, but the signal-to-noise ratio (SNR) is extremely low which limits the application of the method. Most of the current researches focus on eliminating spikes and powerline harmonic noise in the MRS signal, whereas the influence of random noise cannot be ignored even though it is difficult to suppress due to the irregularity. The common method to eliminate MRS random noise is stacking which requires extensive measurement repetition at the cost of detection efficiency, and it is insufficient when employed in a high-level noise surrounding. To solve this problem, we propose a modified short-time Fourier transform(MSTFT) method, in which used is the short-time Fourier transform on the analytical signal instead of the real-valued signal to obtain the high-precision time-frequency distribution of MRS signal, followed by extracting the time-frequency domain peak amplitude and peak phase to reconstruct the signal and suppress the random noise. The performance of the proposed method is tested on synthetic envelope signals and field data. The using of the MSTFT method to handle a single recording can suppress the random noise and extract MRS signals when SNR is more than –17.21 dB. Compared with the stacking method, the MSTFT achieves an 27.88dB increase of SNR and more accurate parameter estimation. The findings of this study lay a good foundation for obtaining exact groundwater distribution by utilizing magnetic resonance sounding.