Magnetorheological elastomer (MRE) is a type of smart material of which mechanical and electrical properties can be reversibly controlled by the magnetic field. In this study, the influence of the magnetic field on the surface roughness of MRE was studied by the microscopic modeling method, and the influence of controllable characteristics of the MRE surface on its friction properties was analyzed by the macroscopic experimental method. First, on the basis of existing studies, an improved mesoscopic model based on magneto-mechanical coupling analysis was proposed. The initial surface morphology of MRE was characterized by the W-M fractal function, and the change process of the surface microstructures of MRE, induced by the magnetic interaction between particles, was studied. Then, after analyzing the simulation results, it is found that with the increase in the magnetic field and decrease in the modulus of rubber matrix, the surface of MRE changes more significantly, and the best particle volume fraction is within 7.5%-9%. Furthermore, through experimental observation, it is found that the height of the convex peak on the surface of MRE decreases significantly with the action of the magnetic field, resulting in a reduction in the surface roughness. Consistent with the simulation results, a particle volume fraction of 10% corresponds to a maximum change of 14%. Finally, the macroscopic friction experiment results show that the friction coefficients of MREs with different particle volume fractions all decrease with the decrease in surface roughness under the magnetic field. When the particle volume fraction is 10%, the friction coefficient can decrease by 24.7% under a magnetic field of 400 mT, which is consistent with the trend of surface roughness changes. This shows that the change in surface morphology with the effect of the magnetic field is an important factor in the control of MRE friction properties by magnetic field.