Shot peening is widely used in engineering as a classical strengthening process. Although many studies on shot peening have been done, most have focused on homogeneous target materials. In this paper, a theoretical model is proposed for predicting the surface morphology of inhomogeneous target materials. The topography of target materials after single-shot impact is calculated on the basis of energy conservation and Hertz contact theory, and the final three-dimensional surface topography after multiple-shot impact is obtained through superposition. Single-shot and random multiple-shot finite element models are used to show the advantages of the proposed model over the existing theoretical model for homogeneous target materials. The roughness is found to increase with the shot velocity and shot radius.