<p>Reconciliation of geodetic observations of short-term deformation and geologic records of long-term deformation is required to better understand the processes of crustal deformation associated with the generation of tectonic landforms and earthquakes. However, there appears to be a discrepancy between these observations in the Niigata–Kobe Tectonic Zone, central Japan, and conventional block-based models are inadequate for explaining the crustal deformation. To investigate this discrepancy, we use satellite positioning data to objectively estimate the three-dimensional distribution of inelastic deformation that causes crustal deformation during an interseismic period. Our results reveal depth-dependent deformation that is distinct from that of the block-based models. Simple rigid block motion in the deep part of the crust, overlain by a complex fault system in the shallow part, consistently explains both the geologic and geodetic deformations. The depth-dependent structure constitutes a new endmember model of crustal deformation that represents less-developed tectonic structures at the opposite end of the deformation spectrum to the block-based models that consider fully developed plate boundaries. Our method effectively integrates geology and geodesy and should contribute to a new conceptualization of tectonic processes.</p> Graphical Abstract <p></p>