The asthenosphere upwelled on a large scale in the western Pacific and South China Sea during the Cenozoic, which formed strong upward throughflow and caused the thermal structure to be changed obviously. The mathematical analysis has demonstrated that the upward throughflow velocity may have varied from 3×1011 to 6×1012 m/s. From the relationship between the lithospheric thickness and the conductive heat flux, the lithospheric heat flux in the western Pacific should be above 30 mW/m2, which is consistent with the observed data. The huge low-speed zone within the upper mantle of the marginal sea in the western Pacific reflects that the upper mantle melts partially, flows regionally in the regional stress field, forms the upward heat flux at its bottom, and causes the change of the litho-spheric thermal structure in the region. The numerical simulation result of the expansion and evolution in the South China Sea has demonstrated that in the early expansion, the upward throughflow velocity was relatively fast, and the effect that it had on the thickness of the lithosphere was relatively great,resulting in the mid-ocean basin expanding rap-idly. After the formation of the ocean basin in the South China Sea, the upward throughflow velocity decreased, but the conductive heat flux was relatively high, which is close to the actual situation. Therefore, from the heat transfer point of view, this article discusses how the up-ward heat flux affects the lithospheric thermal structure in the western Pacific and South China Sea. The conclusions show that the upward heatthroughflow at the bottom of the lithospheric mantle resulted in the tectonic deformation at the shallow crust. The intensive uplifts and rifts at the crust led to the continent cracks and the expansion in the South China Sea. The asthenosphere upwelled on a large scale in the western Pacific and South China Sea during the Cenozoic, which formed strong upward throughflow and caused the thermal structure to be changed obviously. The mathematical analysis has been the upward throughflow velocity may have varied from 3 × 1011 to 6 × 1012 m / s. From the relationship between the lithospheric thickness and the conductive heat flux, the lithospheric heat flux in the western Pacific should be above 30 mW / m2, which is consistent with the observed data. The huge low- speed zone within the upper mantle of the marginal sea in the western Pacific corresponds that the upper mantle melts partially, flows regionally in the regional stress field, forms the upward heat flux at its bottom, and causes the change of the litho-spheric thermal structure in the region. The numerical simulation result of the expansion and evolution in the South China Sea has been demonstrated that in the early expansion, the upward throughflow velo city ​​was relatively fast, and the effect that it had on the thickness of the lithosphere was relatively great, resulting in the mid-ocean basin expanding rap-idly. After the formation of the ocean basin in the South China Sea, the upward throughflow velocity decreased, but the conductive heat flux was relatively high, which is close to the actual situation. Therefore, from the heat transfer point of view, this article discusses how the up-ward heat flux affects the lithospheric thermal structure in the western Pacific and South The settled show that the upward heatthroughflow at the bottom of the lithospheric mantle resulted in the tectonic deformation at the shallow crust. The intensive uplifts and rifts at the crust led to the continent cracks and the expansion in the South China Sea.