In order to remove noise generated during the accelerometer calibration process, an accelerometer denoising method based on empirical mode decomposition (EMD) and time-frequency peak filtering (TFPF) is proposed in this paper. Firstly, a new design of the accelerometer structure is introduced and analyzed by finite element analysis software. Then, an algorithm combining EMD and TFPF is proposed for the first time to deal with the noise of the accelerometer calibration process. Specific steps taken are to remove the intrinsic mode function (IMF) component of the high frequency band after the EMD decomposition, and then to use the TFPF algorithm to process the IMF component of the medium frequency band; meanwhile, the IMF component of the low frequency band is reserved, and finally the signal is reconstructed. The reconstruction results show that the algorithm can effectively suppress the random noise generated during the calibration process. The results of spectrum analysis show that EMD + TFPF can effectively protect the characteristics of the original signal and that the error can be controlled within 0.5%. Finally, Allan variance is used to analyze the results of the three methods to verify the filtering effect. The results show that the filtering effect of EMD + TFPF is the most obvious, being 97.4% higher than the original data.