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A high‐resolution model of three‐dimensional P wave tomography of the crust and upper mantle beneath the southern part of the Philippine Trench is determined by inverting 22,960 arrival times of 2,789 local earthquakes and 4,660 traveltime residuals of 751 teleseismic events simultaneously. The tomographic method TOMOG3D is used to obtain the tomographic model that has a lateral resolution of 0.6° or better, as shown by extensive checkerboard resolution tests. A model‐recovery synthetic test is also performed, which indicates that main features of our tomographic images are quite robust. Our results show that the Philippine Sea slab has subducted down to depths of 450–600 km with an overturned dip angle along the southern segment of the Philippine Trench, indicating that the subduction of the Philippine Sea Plate along the southern segment of the Philippine Trench initiated at 20–25 Ma, contemporaneous with the Sangihe Trench. The subduction initiation of the Philippine Sea Plate at the central Philippine Trench resulted from the collision between the Philippines and the Palawan block at ~10 Ma. The subduction completion of the Molucca Sea slab propagated from the south to the north at ~5 Ma, which presumably resulted in the subduction reorganization of the Philippine Sea Plate along the southern segment of the Philippine Trench and subduction initiation of the Philippine Sea Plate along the northern segment of the Philippine Trench.