The South China Sea is in the convergence zone of the Pacific plate, the Indo-Australian plate, and the Eurasian plate. Its formation and tectonic evolution were influenced by continental margin spreading and plate interaction between the three plates and their microcontinents. It has a complex geodynamic background. To understand how continents break up to form ocean basins, the South China Sea Basin is taken as an example to study the dynamic mechanism of its formation and evolution and the driving force of seafloor spreading, so as to understand the relationship between oceanic–continental lithosphere plates. The South China Sea basin’s opening mechanism and its principal factors of control remain controversial. To explore the influence of different extension rates, we summarized the different genesis mechanisms of the South China Sea, and combined with the tectonic section of the basin, the numerical simulation was obtained based on the finite difference method. The results obtained from numerical simulations show that the rapid extension rate was one of the important factors in the asymmetric expansion of the model, with other factors such as the thickness and rheological properties of the lithosphere held constant. The lithospheric mantle continued thinning in the stress concentration area, with the crust being pulled apart before the lithospheric mantle, eventually forming an ocean basin corresponding to the east sub-basin. However, when the extension rate was low, the model expanded almost symmetrically, and the lithosphere thinning occurred at a slow rate. The simulation results confirm that, compared with the southwest sub-basin of the South China Sea, the spreading rate of the east sub-basin was even higher. We believe that the subduction of the proto-South China Sea played a crucial role in the opening of the South China Sea, providing a more reasonable mechanism. The opposite movement of the Indo-Australian plate and Kalimantan may have inhibited the formation of the southwest sub-basin of the South China Sea, resulting in a later spreading of the southwest sub-basin than the east sub-basin, as well as a lower rate of spreading than the east sub-basin.