The extensive intraplate seamounts are obvious features in the northern South China Sea (SCS). However, the distribution, volume, and origin of these seamounts are not well understood, which greatly hinders our understanding of magmatism in the SCS. Based on high‐resolution bathymetric data and 147 seismic profiles, and combining gravity and magnetic data, we first identify 45 seamounts in the northern margin of the SCS and simulate their shape with elliptical cones. Results show that the total volume of these 45 seamounts above seafloor is estimated at about 1885–3078 km3 and the total volume of intrusive magma above Moho is about 0.15 Mkm3, which is close to the estimates for classic large igneous provinces across the world. These seamounts are mostly located on the continental slope with thin crust (approximately 12–18 km), which reduces the overlying pressure and shortens the magmatic conduits. The dominant azimuth of elliptical major axis in seamounts is consistent with the synrift and synspreading fault strikes (NE‐NEE), indicating that these preexisting faults provide magmatic conduits for the subsequent postrift intraplate seamounts. Based on three existing clues, i.e., (1) the intraplate seamounts, high velocity layer and Hainan mantle plume are contiguous in 3‐D space, (2) the high‐velocity layer is thicker beneath the continental shelf but thinner beneath the slope, and (3) the basalts dredged from certain seamounts show OIB‐type geochemical features, we propose a magmatic upwelling pattern which contains Hainan mantle plume to explain the spatial and morphological characteristics of these intraplate seamounts.