The 6.6 Hokkaido Eastern Iburi earthquake striking southern Hokkaido Island on 5 September 2018 was a disastrous and peculiar event. In contrast to the usually shallow crustal earthquakes, this event occurred at a hypocentral depth about 37 km, close to the Moho discontinuity. To infer the rupture feature of the 2018 Hokkaido earthquake, we determine focal mechanism and centroid depth of the event with inversion of teleseismic waveforms. The result reveals that the centroid (at depth about 26 km) of this thrust earthquake is shallower than the hypocenter, which suggests the upward rupture propagation and dominant rupture in the lower crust. We also investigate the causative fault and rupture directivity based on waveform modeling. The steeply dipping fault (70°) with strike in the north–south direction is preferred to be the causative fault. The total dimension of rupture is estimated to be about 30 km, based on the aftershock distribution and rupture directivity. We propose that a seismogenic model with low temperature and complex stress field in the lower crust above the subduction‐zone interface may explain this event.