Abstract: With the statistic results about a total of 392 geothermal gradient values and 234 heat flow values, the geothermal gradients range from 2.94℃/hm to 5.22℃/hm with an average of 3.91±0.74℃/hm, and the heat flow values vary from 24.2 mW/m² to 121 mW/m² with an average of 77.5±14.8 mW/m² in the deep-water area of the northern South China Sea. The present geothermal field in the deep-water area of the northern South China Sea is characterized with "hot basin". The heat flow value increases from continental shelf to continental slope against the trend of the crust thickness, its distribution is also characterized with prominent local anomalies. The "hot basin" in the deep-water area of the northern South China Sea might be a result of the combination of the Cenozoic lithospheric thinning with the magma activities and faulting during the Neotectonic event. The variation trend of heat flow value was controlled by the magnitude of the lithospheric thinning. The magma activities and faulting during the Neotectonic period might be the main factors for the existence of the local anomaly of heat flow value.