In order to improve the denoising quality of the pulsar signal, an empirical mode decomposing method (EMD) of pulsar signal denoising based on mode cell proportion shrinking is proposed. Firstly, the pulsar signal is decomposed into a series of intrinsic mode functions (IMF), and the part between the two adjacent zero-crossing within IMF is defined as a mode cell. Then, the optimal proportional shrinking factor is constructed by treating mode cell as the basic unit of analysis. Finally, the all mode cells within IMF are denoised by proportion shrinking, and the mode cell proportion shrinking denoising model is established. The experimental results show that compared with the two EMD denoising algorithms based on coefficient threshold and mode cell threshold, the proposed method can more effectively remove the pulsar signal noise, with better preserving the useful detail information in the original signal.