Abstract: The surface friction between any object can be regarded as the friction between rough surfaces, and most rough surfaces have fractal characteristics. In order to study the friction behavior of fractal rough surface, the molecular dynamics-Green’s function method (GFMD) is used to establish the microscopic fractal rough surface. The contact and friction processes of fractal rough surface are controlled by displacement loading, and the contact cluster distribution is identified by breadth-first search algorithm. Then, the maximum friction coefficient and friction force at atomic scale, contact cluster scale and interface scale are calculated respectively. The influence matrix method is used to study the interaction between contact clusters in the friction process, and the influence of the distance between contact clusters and the area of contact clusters on the interaction is analyzed. The results show that the friction coefficient decreases from small scale to large scale during the friction process. The friction force fluctuates periodically with the displacement. The contact clusters don’t reach the maximum friction force at the same time, but local slip occurs. The contact clusters slipping first will accelerate the slip of other contact clusters, and the friction force obtained by the global slip model is the upper limit of the molecular simulation results. The influence matrix method can simulate the interaction of contact clusters well. The maximum friction force calculated by using the influence matrix is basically consistent with the result of GFMD model, and the maximum friction force calculated by ignoring the influence of local slip is 20% larger than the result of GFMD model, indicating that local slip has a great influence on the friction force. The interaction between contact clusters is inversely proportional to the distance and proportional to the area. The results can provide theoretical basis for interface analysis and optimization of fractal rough surface.