To determine the exact location of the Mesozoic subduction zone in the northern South China Sea, the LCT joint inversion software is used to process gravity and magnetic data. The results show that there is a high horizontal-gradient of Bouguer gravity anomaly zone from southwestern Taiwan to the east of Yitongansha uplift, which may indicate the location of the ancient subduction, and there is a high magnetic anomaly zone parallel the gravity anomaly suggesting a Mesozoic volcanic arc which corresponds to the subduction. Well information proves that the subduction took place from the Late Jurassic to Early Cretaceous. Based on all above, the authors draw the tectonopaleogeographic evolution map of the South China Sea from Late Mesozoic to present day, and argue that the ancient subduction zone was a pre-existing weak band controlled the initial position of the spreading of the South China Sea oceanic basin.