Spreading magnetic anomalies recorded the paleo-geomagnetic field variation that has great significance in the investigation of the extension process of ocean basins. Interpreting spreading magnetic anomalies under complex geological environments is challenging, especially for marginal sea basins. We proposed nested elliptical directional filters to separate the spreading magnetic anomalies of the South China Sea (SCS). The results show that the spreading magnetic anomalies separated by the nested elliptical directional filters depict the expansion process of the oceanic crust, and the interference magnetic anomalies are effectively suppressed. The separated spreading magnetic anomalies indicate that the expansion process of the SCS is affected by the interactions between the surrounding plates. The spreading magnetic anomalies of the SCS are warped, interrupted, and not strictly parallel. The pattern of the spreading magnetic anomalies reflects multiple ridge jumps during the expansion process and the post-spreading magmatic disturbances. The long-wavelength magnetic anomalies indicate lithospheric fractures and Curie surface variations in the SCS, which are affected by the post-spreading magmatic rejuvenation. The magnetic anomalies of the SCS resulted from the superposition of magnetic anomalies in the ocean crust and the uppermost mantle.