The magnetic anomaly map shows an obvious NE-SW trending high-amplitude magnetic anomaly zone (NSCSMA) in the northern South China Sea (SCS) continental margin that extends from southwest Taiwan to the area at approximately 114°E and 20°N. The origin of this high-amplitude magnetic anomaly zone is important for understanding the magmatism, margin rifting, and tectonic evolution of the SCS. To gain insight into this issue, in this study, wavelet spectrum analysis, 2D magnetic modeling, and compact inversion were used to identify the causal source of the NSCSMA. Combining wavelet spectrum analysis with magnetic modeling results, we find that the depths of the major magnetic sources are not consistent along the strike of the NSCSMA (∼15 km in the east and ∼25 km in the west). The compact inversion results along five profiles across the NSCSMA also revealed two kinds of geometries (quasi-dike in the east and dome-like in the west) of the causal sources of the NSCSMA with different depths. Based on our findings and previous paleo-subduction model, we propose that the major source of the NSCSMA is serpentinized upper mantle materials associated with paleo-Pacific plate subduction.