Abstract Tolerance analysis plays an important role in predicting the quality of mechanical products in early design stage. However, previous researches on tolerance analysis have mostly ignored the effects of contact behaviors between mating surfaces. This may lead to unrealistic results, especially when analyzing products with kinematic pairs such as rotating mechanisms. In order to obtain more accurate and realistic analysis results, this paper proposes a tolerance analysis approach that considers the effects of contact behaviors between mating surfaces. Geometric features with machining and assembly errors are modeled based on the concept of Skin Model Shapes. Contact behaviors between mating surfaces are calculated by the Conjugate Gradient-Fast Fourier Transform (CG-FFT) method, a classic Boundary Element Method (BEM) for solving contact problems. On these bases, a cam mechanism is adopted as an example to illustrate the effects of contact behaviors on transmission performance. Through the tolerance analysis, not only the transmission error of cam mechanism is analyzed, but also the contact status and pressure distribution between kinematic pairs can be obtained, which provide references for other aspects such as reliability analysis.