The South Yellow Sea Basin is partially surrounded by the East Asian continental Meso-Cenozoic widespread igneous rocks belt. Magnetic anomaly and multi-channel seismic data both reveal the prevalent occurrence of igneous rocks. We preliminarily defined the coupling relation between magnetic anomalies and igneous rock bodies. Some igneous complexes were also recognized by using multi-channel seismic and drilling data. We identified various intrusive and extrusive igneous rock bodies, such as stocks, sills, dikes, laccoliths and volcanic edifice relics through seismic facies analysis. We also forecasted the distribution characteristics of igneous complexes. More than fifty hypabyssal intrusions and volcanic relics were delineated based on the interpretation of magnetic anomaly and dense intersecting multi-channel seismic data. It is an important supplement to regional geology and basin evolution research. Spatial matching relations between igneous rock belts and fractures document that extensional N–E and N–NE-trending deep fractures may be effective pathways for magma intrusion. These fractures formed under the influence of regional extension during the Meso-Cenozoic after the Indosinian movement. Isotopic ages and crosscutting relations between igneous rock bodies and the surrounding bedded sedimentary strata both indicate that igneous activities might have initiated during the Late Jurassic, peaked in the Early Cretaceous, gradually weakened in the Late Cretaceous, and continued until the Miocene. Combined with previous studies, it is considered that the Meso-Cenozoic igneous activities, especially the intensive igneous activity of the Early Cretaceous, are closely associated with the subduction of the Paleo-Pacific Plate.