As the only convergent boundary in the eastern South China Sea (SCS), the Manila subduction zone is a key to understand the subduction mechanism of the SCS and to deepen the tectonic evolution of the SCS from marginal breakup, via spreading to closure. The latest tomographic images show that the original range of the SCS extends from the present Manila Trench eastward to 400 500km. However, the initial time of the SCS subduction is controversial and the subduction mechanism is poorly understood. Based on the seismic profiles across the Manila subduction zone, the ages of igneous rocks, and the results of balanced cross-sections, this paper systematically analyzes and defines the segmentation and initial subduction time. This study found that the zircon age data distributed in the Philippine Islands are mainly in the Early Miocene-Middle Miocene period, and the balanced profile analysis shows that the SCS subduction has begun in the Middle Miocene. Therefore, the initial subduction time is proposed to be from Early Miocene to Middle Miocene, and the subduction migrated from south to north. Combined with the results of the Cenozoic plate reconstruction around the SCS, the evolution of the Manila subduction zone can be subdivided into three stages: (1) During the Paleocene-Early Miocene, the Manila subduction zone existed as a large-scale strike-slip fault zone or subduction zone boundary. (2) In the Early Miocene-Middle Miocene, under the background of multiple plate convergence, due to the joint effect of the rapid northward movement of the Australian Plate, the WNW-directed subduction of the Pacific Plate, and the WNW-directed drift of the Philippine Sea Plate which collided with the North Palawan Microplate (Mindoro), the large-scale strike-slip boundary in the western Philippine began to form as the Manila subduction zone, and the SCS began its subduction. (3) During the Late Miocene-Early Pleistocene, as the Philippine Sea Plate continued to move northwestward, the northern segment of the Manila subduction zone entered a collisional orogenic stage, while the southern segment was still in a state of oceanic crust subduction. This process eventually formed the present-day trench-accretionary wedge-forearc basins (North Luzon Trough and West Luzon Trough)-volcanic arc (Luzon Volcanic Arc) geomorphological combination. In summary, the extinction of the SCS is passive, because the Manila subduction zone belongs to the dynamic system of the Pacific Plate and is caused by induced passive subduction, different from the Sumatra-Banda subduction zone triggered by active subduction of the Indian-Australia Plate dynamic system. However, both subduction zones shape the circular Southeast Asian subduction system together.