To solve the difficult problem of low-frequency noise processing in pipeline infrasonic leakage detection signals, a pipeline infrasonic leakage signal denoising method based on improved Prony algorithm and differential energy model was proposed to reduce the low-frequency interference noise in the signal and to improve the signal denoising effect. First, the frequency window of the effective signal is obtained according to the spectrogram of the infrasound signal. Aiming at the problem that the Prony algorithm is affected by noise, a difference energy model is proposed. The difference energy model is used to filter out the part of the frequency domain signal with large energy fluctuation, and a relatively stable preprocessing signal is obtained. In view of the instability of the traditional Prony algorithm, a Hankel matrix is established in the operation process. The stability is improved by extracting the extremum and residue of the signal instead of directly solving the sampling data points, and the extremum and residue of the effective signal are selected by combining the frequency window of the active ingredient. Finally, the effective signal is reconstructed to obtain a relatively stable infrasound leakage noise reduction signal. Experimental results show that the noise reduction technology based on the improved Prony algorithm and differential energy model can effectively reduce the noise of pipeline leakage signals. Compared with the traditional Prony algorithm, the noise reduction effect of the proposed method is up to 38.01% higher. Compared with the empirical mode decomposition method, the noise reduction effect of this method is improved by 9.25% at least, which opens up a new idea for pipeline leakage signal noise reduction.