Abstract: Rough contact is a prerequisite for surface friction. The rough contact behaviour such as the contact area, the pressure distribution and spatial distributions has been one of the core issues in contact mechanics and tribology. In this paper, the molecular dynamics-Green's function method (GFMD) is used to simulate the contact mechanism of the rough surface, where the asperity model is used for the rough surface, i.e., the surface is composed of numerous spherical asperities. Starting with the atomic or molecular force filed to consider the rough contact behaviour, the molecular dynamics-Green's function method is able to capture the mechanisms such as super-lubrication and multi-scale effect behaviour, which are not found in traditional continuum mechanics. The molecular dynamics-Green's function method demonstrates its high efficiency in large scale molecular dynamics simulations and is able to simulate the system composed of billions of atoms. The results of single asperity contact based on Hertz contact theory are very close to those simulated by the molecular dynamics-Green's function method, and the difference is less than 5%. It is found by numerical simulation that the contact area is linearly related to the contact force if the asperity heights follow the Gaussian distribution, and the contact force obtained by the asperity model is the upper limit given the same contact area. Although Asperity model is fast, it overestimates the stiffness of the elastomer due to the neglection of the interaction between the asperities. In real contact process, asperities have considerable effects on each other, especially on the deformation of the adjacent area, which makes the contact spots more discrete. The information of the real contact area and its spatial distributions, is of importance for the following simulation on surface friction.