A contact model with refined surface topography is important to the frictional wear study of rubber seal. But the traditional modeling method relies on the measurement of surface characteristics of rubber material, which increases the cost due to high-precision instruments and complex data processing. In the paper, a new modeling method on reconstructing the 3D surface topography is proposed. The coordinate cloud of the surface is generated based on the random distribution of asperity height, which is established according to the initiate parameters of the surface roughness. The metal-rubber assembly model with 3D topography of rough surfaces are built. The simulation on metal-rubber contact behavior is conducted in ANSYS. The result shows a power-exponent relation is between the real contact area and the external pressure, and three contact states of no contact, adhesion and slippage are defined to describe the dynamic distribution of real contact area. The authors proved the reliability of the topography reconstruction method by an indentation experiment on rubber material. The area ratio reflects not only the change rule of contact area under an increasing pressure, but also the difference of contact behavior of the contact pairs under different surface roughness.