The shaft centerline orbit contains abundant information about fault symptoms, but the measured orbit is often confused by the interference of noise. Based on partial differential equation (PDE), this paper proposes a method for purification of the shaft centerline orbit to overcome the shortcomings of the traditional method. We analyze the principle of filtering based on PDE，PDE filter parameter design and its numerical process. Its correlativity is discussed with the traditional filter and realized the purification of the shaft centerline orbit. Experiment results show that the method is a flexible method of denoise, can effectively eliminate the noise disturbing , also avoid signal distortions after denoise, and at the same time keep the property of signal.