Quantitative analysis of radiolarian preservation in surface sediments from different regional environments of the South China Sea (SCS) is discussed in this article for illustrating their relationship. The results show that species diversity and abundance of radiolarian in the surface sediment increase with water depth, indicating no obvious dissolution of radiolarian shell in the deep SCS. Upwelling activity and volcanic eruption are both in favor of radiolarian propagation, and cause the settlement enrichment of radiolarian shell. Whereas, an abnormal reduced radiolarian fauna in deeper slope sediment may result from the remain of turbid flow that brings sediments from shallow area, such as shelf and upper slope. Radiolarian species are mainly composed of tropic-subtropic types, and include some cold or polar species, which indicates that a mistake in paleoceanographic analysis should arise from the monospecific index. However, synthesis radiolarian indexes in sediments may well respond to the ecologic and depositional environments in the SCS.