This paper proposes a waveform inversion analysis for three‐dimensional (3D) crust structure modeling considering the effect of surface topography. In order to compute the sensitivity functions, we use a 3D finite‐element method (FEM) based on a hybrid grid, which can improve the accuracy in surface and interface modeling, and reduce the computation cost of modeling and analysis. The applicability of the method is examined by modeling the interface between a sedimentary layer and seismic bedrock. We then demonstrate the advantage of our method by comparing 3D models with and without consideration of surface topography. The results confirm the existence of significant surface topography effects and show that our method can accurately estimate 3D crust structures even with such topographic effects.