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It is of great significance to construct a three-dimensional underground velocity model for the study of geodynamics and tectonic evolution. Southeast Asia has attracted much attention due to its complex structural features. In this paper, we collected relative travel time residuals data for 394 stations distributed in Southeast Asia from 2006 to 2019, and 14,011 seismic events were obtained. Then, teleseismic tomography was applied by using relative travel time residuals data to invert the velocity where the fast marching method (FMM) and subspace method were used for every iteration. A novel 3D P-wave velocity model beneath Southeast Asia down to 720 km was obtained using this approach. The tomographic results suggest that the southeastern Tibetan Plateau, the Philippines, Sumatra, and Java, and the deep part of Borneo exhibit high velocity anomalies, while low velocity anomalies were found in the deep part of the South China Sea (SCS) basin and in the shallow part of Borneo and areas near the subduction zone. High velocity anomalies can be correlated to subduction plates and stable land masses, while low velocity anomalies can be correlated to island arcs and upwelling of mantle material caused by subduction plates. We found a southward subducting high velocity body in the Nansha Trough, which was presumed to be a remnant of the subduction of the Dangerous Grounds into Borneo. It is further inferred that the Nansha Trough and the Dangerous Grounds belong to the same tectonic unit. According to the tomographic images, a high velocity body is located in the deep underground of Indochina–Natuna Island–Borneo–Palawan, depth range from 240 km to 660 km. The location of the high velocity body is consistent with the distribution range of the ophiolite belt, so we speculate that the high velocity body is the remnant of thee Proto-South China Sea (PSCS) and Paleo-Tethys. This paper conjectures that the PSCS was the southern branch of Paleo-Tethys and the gateway between Paleo-Tethys and the Paleo-Pacific Ocean. Due to the squeeze of the Australian plate, PSCS closed from west to east in a scissor style, and was eventually extinct under Borneo. [ABSTRACT FROM AUTHOR]