As one of the most widely used core parts in mechanical products, the shaft and hole parts tend to develop towards high precision, high strength and diversity. The quality control and quality evaluation are very important for shaft and hole parts. For the shape error separation of the shaft and hole parts, a harmonic separation method is proposed based on the research on the traditional error separation technique and the harmonic theory. According to the periodic data measured on the parts, the generation mechanism of each harmonic error is analyzed, and the measures to reduce the error are put forward. The actual position of the measuring point is obtained by using the space point vector method, and the surface topographies of the parts are predicted by combining with the surface fitting algorithm. The accuracy and rationality of the harmonic separation and surface topography prediction method are verified by experiments. Those methods provide a new idea for the surface quality evaluation and prediction of shaft and hole parts.