High-G MEMS accelerometer (HGMA) is a new type of sensor; it has been widely used in high precision measurement and control fields. Inevitably, the accelerometer output signal contains random noise caused by the accelerometer itself, the hardware circuit and other aspects. In order to denoise the HGMA’s output signal to improve the measurement accuracy, the improved VMD and TFPF hybrid denoising algorithm is proposed, which combines variational modal decomposition (VMD) and time-frequency peak filtering (TFPF). Firstly, VMD was optimized by the multi-objective particle swarm optimization (MOPSO), then the best decomposition parameters [kbest,abest] could be obtained, in which the permutation entropy (PE) and fuzzy entropy (FE) were selected for MOPSO as fitness functions. Secondly, the accelerometer voltage output signals were decomposed by the improved VMD, then some intrinsic mode functions (IMFs) were achieved. Thirdly, sample entropy (SE) was introduced to classify those IMFs into information-dominated IMFs or noise-dominated IMFs. Then, the short-window TFPF was selected for denoising information-dominated IMFs, while the long-window TFPF was selected for denoising noise-dominated IMFs, which can make denoising more targeted. After reconstruction, we obtained the accelerometer denoising signal. The denoising results of different denoising algorithms in the time and frequency domains were compared, and SNR and RMSE were taken as denoising indicators. The improved VMD and TFPF denoising method has a smaller signal distortion and stronger denoising ability, so it can be adopted to denoise the output signal of the High-G MEMS accelerometer to improve its accuracy.