Heat flow plays an important role in the study of thermal structure and thermal evolution of continental margin of the northern South China Sea. The analysis of heat flow value shows that margin heat flow in the northern South China Sea is relatively high setting, but the percentage of crustal heat flow is lower than 35% in terrestrial heat flow. The terrestrial heat flow exhibited a current of rise from the Northern Continental Margin to the Southern Central Basin. However, the proportion of crustal heat flow in terrestrial heat flow slowly dropped down in the same direction. It is suggested that the main factor causing high heat flow setting is the moving up of hot material from asthenosphere.