The northern margin of the South China Sea (SCS) is often regarded as a magma-poor passive continental margin. Magmatic activities occurred after the cessation of seafloor spreading were founded mainly over the Continent-Ocean Transition (COT) zone. Intrusive rocks are observed in the Luzon–Ryukyu Transform Plate Boundary (LRTPB) dividing Southwest Taiwan Basin (SWTB) and Pearl River Mouth Basin (PRMB) north of the COT and their evolution mechanisms are not very well-studied. Here, detailed structural and geophysical features of a large-scale anomaly (LSA) is revealed from high-resolution multi-channel seismic (MCS) profiles over the LRTPB dividing the SWTB and the PRMB. After velocity estimation, AVO analysis, and geological interpretation for the LSA, we suggest that the LSA is an intrusive igneous rock and further classified as a laccolith. The coexistence of the laccolith and surrounding sills over the LRTPB shows that the north limit of magmatism is further north than the COT zone. The elongated shape of the laccolith is accordant to the NW directional LRTPB, indicating that magmatic activities of study region maybe controlled by the faulting.