Interplate megathrust earthquakes have inflicted catastrophic damage on human society. Such an earthquake is predicted to occur in the near future along the Nankai Trough off southwestern Japan—an economically active and densely populated area in which megathrust earthquakes have already occurred1,2,3,4,5. Megathrust earthquakes are the result of a plate-subduction mechanism and occur at slip-deficit regions (also known as ‘coupling’ regions)6,7, where friction prevents plates from slipping against each other and the accumulated energy is eventually released forcefully. Many studies have attempted to capture distributions of slip-deficit rates (SDRs) in order to predict earthquakes8,9,10. However, these studies could not obtain a complete view of the earthquake source region, because they had no seafloor geodetic data. The Hydrographic and Oceanographic Department of the Japan Coast Guard (JHOD) has been developing a precise and sustainable seafloor geodetic observation network11in this subduction zone to obtain information related to offshore SDRs. Here, we present seafloor geodetic observation data and an offshore interplate SDR-distribution model. Our data suggest that most offshore regions in this subduction zone have positive SDRs. Specifically, our observations indicate previously unknown regions of high SDR that will be important for tsunami disaster mitigation, and regions of low SDR that are consistent with distributions of shallow slow earthquakes and subducting seamounts. This is the first direct evidence that coupling conditions might be related to these seismological and geological phenomena. Our findings provide information for inferring megathrust earthquake scenarios and interpreting research on the Nankai Trough subduction zone.