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The whole rock K-Ar ages of basalts from the South China Sea basin vary from 3.8 to 7.9 Ma, which suggest that intra-plate volcanism after the cessation of spreading of the South China Sea (SCS) is comparable to that in adjacent regions around the SCS, i.e., Leiqiong Peninsula, northern margin of the SCS, Indochina block, and so on. Based on detailed petrographic studies, we selected many fresh basaltic rocks and measured their major element, trace element, and Sr-Nd-Pb isotope compositions. Geochemical characteristics of major element and trace element show that these basaltic rocks belong to alkali basalt magma series, and are similar to OIB-type basalt. The extent of partial melting of mantle rock in source region is very low, and magma may experience crystallization differentiation and cumulation during the ascent to or storing in the high-level magma chamber. Sr-Nd-Pb isotopic data of these basaltic rocks imply an inhomogeneous mantle below the South China Sea. The nature of magma origin has a two end-member mixing model, one is EM2 (Enriched Mantle 2) which may be originated from mantle plume, the other is DMM (Depleted MORB Mantle). Pb isotopic characteristics show the Dupal anomaly in the South China Sea, and combined with newly found Dupal anomaly at Gakkel ridge in Arctic Ocean, this implies that Dupal anomaly is not only limited to South Hemisphere. In variation diagrams among Sr, Nd and Pb, the origin nature of mantle below the SCS is similar to those below Leiqiong peninsula, northern margin of the SCS and Indochina peninsula, and is different from those below north and northeast China. This study provides geochemical constraints on Hainan mantle plume.