Three dimensional P-wave and S-wave velocity structure in the Unzen volcanic region, southwest Japan was estimated with the arrival time data of local earthquakes. A broad low velocity anomaly crosses the volcanic region from northwest to southeast and dips gradually to southeast. The southeastern deepest portion of the low velocity anomaly coincides with a clear seismicity gap and a prominent low Bouguer gravity anomaly off the Shimabara peninsula. This may suggest the existence of magma activity southeastern portion off the Shimabara peninsula in addition to a magma body under the Chijiwa bay, which has been inferred from previous geological research. The geology of central Kyushu is dominated by the Beppu-Shimabara graben that trends roughly east to west through the center of the studying area. This structure is not apparent in our results, which may mean that the velocity contrasts that define the graben boundaries are too small to be clarified with our data set.