Abstract Reliable calculations of coseismic sea‐surface deformation and stress drop are essential for understanding megathrust earthquake rupture and tsunami behavior. However, the impacts of realistic three‐dimensional (3D) structure, such as seafloor topography and structural heterogeneity, on stress‐change calculations and tsunami excitation during the 2011 Tohoku earthquake have not been fully explored. In this study, we conduct slip inversion analysis using the 3D structure, which reduces the maximum slip by ∼20% and shifts its peak ∼20 km landward relative to homogeneous half‐space modeling, while preserving the magnitude and average stress drop. A 3D finite‐element analysis also shows that tsunami excitation is significantly affected by seafloor topography, whereas subsurface elastic heterogeneity has only a minor effect. In contrast, stress drop on the fault is modulated by along‐strike variations in both factors. These results indicate that half‐space assumptions capture the first‐order rupture characteristics but can introduce significant bias in detailed rupture processes.