The Java subduction zone is located in the southern part of Southeast Asia, where the strong plate convergence results in clustered arc volcanoes and intense seismicity. To better understand the arc magmatism and seismogenesis in this region, we determine a high-resolution 3-D P-wave velocity (Vp) model of the crust and upper mantle down to 600 km depth beneath Java. The geometry of the subducting Australian slab is taken into account in the starting model to obtain a better tomographic result by inverting a large number of travel-time data of local and teleseismic events. Our results show lower intra-slab Vp anomalies at depths of ∼100–200 km than other parts of the slab, which may reflect dehydration embrittlement and a slab hole. Feeble low-Vp anomalies appear below the subducting Australian slab, which is probably due to the slab hole where subslab hot materials flow into the mantle wedge. This feature may be related to the occurrence of potassium-rich back-arc volcanoes and the lack of giant megathrust earthquakes (Mw ≥ 8.5) in Java. Our tomographic results also support the hot finger model for explaining the arc magmatism in Java. •A detailed 3-D P wave velocity model of the Java subduction zone is determined.•The distribution pattern of low-velocity zones in the mantle wedge supports the hot finger model.•A lower-Vp anomaly exists within the high-V slab that is smaller than the well-known seismicity gap.