Accurately characterizing the surface topography of parts is crucial to improve the surface measurement accuracy and analyze the surface contact performance. A method is proposed to separate the morphological characteristics of the actual machined surface based on the layer-by-layer error reconstruction method and the signal-to-noise ratio method during the wavelet transform process, so as to evaluate the contact performance of the different joint surfaces. First, the actual machined surface morphological features are separated by using the wavelet transform method, the layer-by-layer error reconstruction method, and the signal-to-noise ratio method. Second, the reconstructed three-dimensional surface contact model is established by the reverse modeling engineering method. Third, the finite element method is used to analyze the impact of processing methods and surface roughness on contact surface parameters. The result demonstrates that the simplified and efficient three-dimensional reconstructed surface is achieved based on the real machining surface in contrast to other existing approaches. The surface roughness has a more significant influence on contact performance. The contact deformation increases with the increase of surface roughness, while the curves of average contact stress, contact stiffness, and contact area have the opposite trend.