To map the present distribution of sedimentary diatoms, a new data set on the relative abundance of diatom species preserved in 1266 surface sediment samples is generated, which covers the environmental factor characteristic of the central and northern parts of South China Sea (SCS) between 12° and 24°N. The biogeographic distribution patterns of as well as the preferences for environmental variables for 19 diatom species are documented. The relative abundance patterns of the major diatom species were statistically compared with six environmental variables, namely the annual sea surface temperature and salinity, dissolved oxygen, and concentrations of three surface nutrients (nitrate, phosphate, silicate). Pearson correlation and redundancy analyses indicated that species correlated so strongly with the environmental factors that six diatom assemblages could be established. Among which, the Paralia sulcata-Actinoptychus undulatus and Cyclotella stylorum-Cyclotella striata-Actinoptychus splendens-Coscinodiscus decrescens assemblages, located on the east and west sides of the Pearl River Estuary on the northern continental shelf of the SCS, respectively, are related to freshwater inputs from the Pearl River and Guangdong coastal current and Kuroshio intrusion. The Cyclotella striata-Paralia sulcate assemblage off the coast of Vietnam is related to the western boundary current of the SCS. The Nitzschia marina-Rhizosolenia bergonii-Azpeitia africana-Chaetoceros messanensis-Fragilariopsis doliolus assemblage in the northeastern SCS is significantly influenced by the Kuroshio intrusion and the SCS warm current and northern slope current. The Azpeitia nodulifera-Nitzschia marina-Hemidiscus cuneiformis and Azpeitia nodulifera-Nitzschia marina-Thalassionema nitzschioides-Cyclotella striata assemblages located on the Xisha Islands and in the SCS deep-water basin, respectively, correlate strongly with the sea surface temperature pattern. Some biological and sedimentological factors may cause stronger effects on diatom distribution, and may mask the influences of environmental variables. © 2020, Editorial Office of Earth Science Frontiers. All right reserved.