On 1 April 2016, an 5.9 ( 6.5) plate‐boundary earthquake occurred in the subduction zone of the Nankai trough, offshore from the Kii Peninsula, southwest Japan. This event is the largest plate‐boundary earthquake to take place in the source region after the Tonankai earthquake of 1944 ( 8.0). In the last half century, moderate‐to‐large earthquakes of this focal type have become very rare in this region; as such, this event provides a good opportunity to investigate the source characteristics related to strong‐motion generation of subduction‐zone plate‐boundary earthquakes in the Nankai trough. In this study, the source model of the earthquake was estimated on the basis of broadband strong‐motion waveform modeling using the empirical Green’s function method. Source parameters of the strong‐motion generation area (SMGA) were optimized via waveform modeling in the frequency range of 0.4–10 Hz. One SMGA is necessary to explain the observed waveforms at offshore and onshore strong‐motion stations. The best estimate of the size of the SMGA was ; this result does not follow the source‐scaling relationship for past plate‐boundary earthquakes along the Japan trench, northeast Japan. The result implies the possibility of differences between the source characteristics of plate‐boundary events in the Nankai trough and those along the Japan trench. This finding provides important information about regional variations of source characteristics in ground‐motion prediction for hazard assessment of future megathrust earthquakes.