Inland crustal earthquakes usually occur in the brittle upper crust (0–20 km depths), but the 6 September 2018 Eastern Iburi earthquake (M 6.7) took place in southern Hokkaido with a focal depth of ~37 km, causing 41 fatalities and serious damage to the local infrastructure. The reason why this event was so deep and its causal mechanism are still unclear. In this work we study the three-dimensional P and S wave seismic attenuation (1/Q) structure in the source zone of the 2018 Iburi earthquake. Our results show that this event occurred at the boundary between the Sorachi-Yezo belt (low Q) and the dipping Northeastern (NE) Japan arc (high Q) that is descending beneath the Kuril arc. The collision between the NE Japan and Kuril arcs as well as fluids from dehydration of the subducting Pacific plate caused this big event and its unusual focal depth. Similar attenuation structures are revealed in source zones of the 1970 Hidaka earthquake (M 6.7) and the 1982 Urakawa-oki earthquake (M 7.1), suggesting that they were caused by similar processes. We think that large earthquakes will take place again on the active thrust faults in southern Hokkaido in the coming decades. Hence, we should pay much attention to the seismic risk and prepare for reduction of earthquake hazards there.