The joint surfaces have a significant effect on the behavior of mechanical structures. Strong demand exists for the development of a model that can include the contact characteristics of joint surfaces. In this article, a new contact model considering asperity interaction and surface waviness is proposed. The roughness and waviness of the surface are separated by the Fourier series, and a contact model for an asperity is first established to obtain the displacement caused by asperity interaction. The joint surface is then treated as the contact between a rough surface and a smooth waviness to obtain a new model which considers asperity interaction and surface waviness. Simulation results show that when the normal load is fixed, the contact deformation decreases with the increasing radius of the waviness peak, but increases with the increasing surface roughness. In addition, asperity interaction will lead to a lower contact stiffness and a larger real contact area. Compared with other models, the results obtained from the proposed model are closer to the experimental results.