AbstractTo clarify the causal mechanisms of megathrust earthquakes, we studied the detailed three‐dimensional P and S wave velocities (V), attenuation (Q), and Poisson's ratio (σ) structures of the Nankai subduction zone in southwest Japan, using a large number of high‐quality arrival time and t* data measured precisely from seismograms of local earthquakes. The suboceanic earthquakes used are relocated precisely using sP depth phase and ocean bottom seismometer data. Our results show the existence of two prominent high‐V, high‐Q, and low‐σ patches separated by low‐V, low‐Q, and high‐σ anomalies in the Nankai megathrust zone. Megathrust earthquakes during 1900 to 2013 nucleated in or around the high‐V, high‐Q, and low‐σ patches, which may represent strongly coupled areas (i.e., asperities) in the megathrust zone. Our results indicate that structural heterogeneities in the megathrust zone, such as the subducting seafloor topography and compositional variations, control the nucleation of the Nankai megathrust earthquakes.