We present the first three-dimensional seismic velocity model of the Hong Kong region, including the Dangan Island fault zone (DIFZ). The crust beneath Hong Kong is predominantly igneous, and is characterized by relatively high seismic velocity. Further south, we observe an elongated velocity anomaly beneath part of the DIFZ where significant seismicity has been recorded. This anomaly demarcates the contrasting seismic velocity structures on the opposite sides of the fault zone from the surface to a depth of at least 20 km, suggesting that the DIFZ extends to the lower crust and dips subvertically. Our model also indicates that there is an abrupt change in the along-strike crustal structure of the fault zone, with a significantly higher seismic velocity in the region west of the seismically active area. We anticipate that this first three-dimensional subsurface tectonic model of Hong Kong and the DIFZ will help assess the influence of crustal heterogeneities on the spatial pattern of intraplate earthquakes in this densely populated region of south China.