Partial discharge (PD) online monitoring is a common technique for high-voltage equipment diagnosis. However, due to field interference, the monitored PD signal contains a lot of noise. Therefore, this paper proposes a novel method by integrating the flower pollination algorithm, variational mode decomposition, and Savitzky–Golay filter (FPA-VMD-SG) to effectively suppress white noise and narrowband noise in the PD signal. Firstly, based on the mean envelope entropy (MEE), the decomposition number and quadratic penalty term of the VMD were optimized by the FPA. The PD signal containing noise was broken down into intrinsic mode functions (IMFs) by optimized parameters. Secondly, the IMFs were classified as the signal component, the noise dominant component, and the noise component according to the kurtosis value. Thirdly, the noise dominant component was denoised using the SG filter, and the denoised signal was mixed with the signal component to reconstruct a new signal. Finally, threshold denoising was used to eliminate residual white noise. To verify the performance of the FPA-VMD-SG method, compared with empirical mode decomposition with wavelet transform (EMD-WT) and adaptive singular value decomposition (ASVD), the denoising results of simulated and real PD signals indicated that the FPA-VMD-SG method had excellent performance.