A denoising method combined with singular value decomposition (SVD) and Variational mode decomposition (VMD) is proposed to eliminate noise in on-site partial discharge (PD) signals from high-voltage electrical equipment. In the Fourier transform power spectrum, periodic narrowband interference was eliminated after SVD was offered to determine the number of singular values of periodic narrowband interference. Then, the PD signal was decomposed into K intrinsic mode function components by VMD. The empirical mode decomposition method was used to determine the K value of white noise’s intrinsic mode function components. An improved 3σ criterion threshold method was proposed to eliminate the residual noise in the PD signal. The denoising method was compared with the other two methods to analyze the denoising effect on the simulation and experimental PD signal. This paper’s denoising method can eliminate periodic narrowband interference and white noise in different PD signals of cavity discharge, corona discharge, and those from the motors’ coil. The denoised PD pulse waveform has a higher signal-to-noise ratio and normalized correlation coefficient and a lower mean square error, indicating that the waveform’s original characteristic remains.