We investigated the evolution of structure and microscopic residual stress at the SiC/Al interface at the atomic scale during nanoindentation by using molecular dynamics simulations. We find that microscopic residual stresses mainly distribute in the interface region, especially the SiC side ranging from 50 to 60 GPa after relaxation. During nanoindentation, there is a large microscopic residual stress concentration at the indentation area. The microscopic residual stress of the SiC side at the indentation area is more serious than that of the Al side. It is found that some SiC atoms in the indentation region are extruded from the SiC side by the indenter, and the fractured SiC atoms are subjected continuously by the indenter, which accelerates the evolution of structure and microscopic residual at the SiC/Al interface. The fractured SiC atoms aggravate the microscopic residual stress concentration at the SiC/Al interface. Al may release some of the microscopic residual stresses by plastic deformation, while the SiC can only reduce the microscopic residual stress by fracture. Therefore, it is necessary to remove the fractured SiC atoms in time to prevent more complex microscopic residual stresses and to improve the machining process of SiC/Al composites.