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The tectonic history of Southeast Asia has been largely shaped by extensive subduction, with thousands of kilometers of lithosphere subducted since the Mesozoic. The tectonics of the Indonesia-Philippines region are particularly complex, with the convergence of the Australian plate from the south, the Indian plate from the west, and the Philippine Sea plate from the east. This region also features several deformation zones involving several microplates, whose kinematic reconstructions remain poorly understood. In this study, we use full-waveform adjoint tomography to elucidate the seismic absolute P- and S-wave velocity structure in the crust and mantle beneath Southeast Asia. We have collected a large waveform dataset from all available broadband seismic stations within and surrounding Southeast Asia, including a dense array in the Philippines. The inversion optimizes the normalized correlation coefficient between observed and synthetic seismograms within individual time windows. This approach allows us to fit regional multipathed waveforms and provides high-resolution seismic velocity images from the crust to depths of about 1000 km. Our model clearly reveals subducting slabs in the upper mantle beneath the Indonesia-Philippines region, including the Sumatra and Java slabs, the opposingly dipping Manila and Philippine Sea slabs, the Sangihe and Halmahera slabs beneath the Molucca Sea, and the Celebes Sea slab. These slabs correlate well with seismicity and show varying depth extents and dip angles. They behave differently when interacting with the mantle transition zone, with the southern Sumatra, Java, and Sangihe slabs clearly penetrating through the 660-km discontinuity. In addition, we identify several detached slab fragments in the upper mantle, including one beneath the Sulu Sea, likely associated with subduction at the Negros trench, and another northwest-dipping structure east of Sulawesi. In the mantle transition zone and lower mantle, we observe several broad fast anomalies beneath the South China Sea and the Philippine Sea plate that are disconnected from shallower slabs. These anomalies may correspond to the subducted Proto-South China Sea slab and the East Asian Sea slab, respectively, as proposed by recent tectonic reconstructions. Furthermore, our model shows a slab-like fast structure in the transition zone and lower mantle beneath northern Borneo, potentially representing a subducted and detached slab from the northwest Borneo Trough. Our high-resolution tomographic images provide new insights on how these slabs interact with the 660 km discontinuity as they have descended into the lower mantle.