The tectonic evolution of the northwestern continental margin of the South China Sea were controlled by many factors, such as the Red River Fault, the Hainan mantle plume and the formation and evolution of the South China Sea. The Yinggehai Basin is located in the northwest of the South China Sea, where thick Cenozoic sediments were deposited. The Cenozoic evolution history of the northwestern continental margin of the South China Sea was recorded in detail in the Yinggehai Basin. However, which factor has mainly controlled the evolution of the Yinggehai Basin since the Cenozoic is still ambiguous. In this paper, 7 drilling wells and 23 simulated wells were selected in the Yinggehai Basin, and the sedimentation rate and subsidence rate of the Yinggehai Basin were reconstructed by empty basin tectonic subsidence analysis method. The deep structure of the Yinggehai Basin was simulated by gravity inversion method based on previous study. The results show that during the rift period, the subsidence rate of the Yinggehai Basin in the north and middle sections is larger than in the south section. There are two stages of “step acceleration subsidence” in the north and middle sections, which are 23–11.7 Ma BP and 11.7 Ma BP–present, respectively. The maximum tectonic subsidence rate can be up to 80 m/Ma in the post rift stage in the north section and about 110 m/Ma in the middle section. The maximum tectonic subsidence rate of the Southern Graben and Uplift is both close to 70 m/Ma during the periods of 11.7–5.7 Ma BP and 15.9–11.7 Ma BP, respectively. The Cenozoic subsidence of the Yinggehai Basin is consistent with the change of sedimentary rate, indicates that tectonic subsidence plays a significant role on sedimentary evolution. According to the results of gravity inversion, it may be lower crust high density anomaly intrusion underlying the Yinggehai Basin. We suggested it may be basic rock according to the drilling basalts in the sediments. By comparing with the subsidence rate of surrounding basins in the South China Sea, the acceleration subsidence in the 15.9–11.7 Ma BP may be related to the disappearance of secondary mantle convection due to the ceasing of the seafloor spreading of the South China Sea. The 5.7 Ma BP–present accelerated subsidence of the Yinggehai Basin may be related to the dextral strike-slip activity of the Red River Fault.