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Abstract The time‐variable features of interseismic deformation in subduction zones are poorly understood and commonly ignored. Here, by incorporating century‐long leveling data and contemporary global navigation satellite systems (GNSS) velocities, we investigate the temporal evolution of interseismic deformation in southwest Japan using two‐dimensional viscoelastic earthquake‐cycle models. We find that a steady‐state continental mantle viscosity of 1019 Pa·s is required to explain these two geodetic data sets. Our preferred model predicts significant variations in the surface velocity field throughout the entire interseismic period due to viscous mantle flow driven by ongoing megathrust locking, indicating that the multiyear GNSS‐derived velocity field represents a snapshot of time‐varying interseismic deformation. The locking depth and locking time exert significant influences on the horizontal and vertical deformation patterns. Our findings highlight the importance of the interseismically relaxing mantle and the necessity of considering such an effect in determining the current locking state along the Nankai subduction zone.