The surface quality of wafers processed by double-sided polishing (DSP) is significantly influenced by pad morphology. However, quantitative analysis remains challenging due to the complexity of dynamic contact conditions and the coupled effects of pressure and trajectory. To address material removal non-uniformity on wafer surfaces during DSP, this study focuses on the pressure–trajectory coupling mechanism and develops a material removal model incorporating pad topography effects. First, a kinematic model is established to derive the relative velocity of any point on the wafer. Secondly, a 3D elastic contact simulation model is constructed based on a linear elastic small-deformation model to obtain spatial pressure distribution under different pad morphologies. The full-cycle transient process is obtained by averaging typical steady-state conditions. A material removal calculation method is proposed by integrating time-dependent relative velocity and dynamic pressure within a modified Preston framework, and the model is validated against experimental results reported in the literature. Simulations and reported experiments demonstrate that pads with varying radial topographies generate differentiated pressure distribution. The results show that wafer radial within-wafer non-uniformity (WIWNU) can be effectively reduced to 1.002 by adjusting pad shape. This study extends the applicability of material removal rate models and provides a predictive framework for precision control in DSP wafer planarization.