Through research of drilling test data in the main basins of northern South China Sea and analysis of aquathermal pressuring experiment under high temperature for sandstone and mudstone sample in the deepwater area of northern South China Sea, this paper comprehensively discusses the vertical distribution characteristics of geotemperature and geopressure under high temperature conditions in the deepwater area of northern South China Sea. The research shows the existence of overpressure geotemperature—geopressure system in high temperature environment of deep layers of Qiongdongnan Basin and Pearl River Mouth Basin in northern South China Sea with exponential relation between geotemperature and geopressure. Different from the traditional “broken line mode”, the geotemperature—geopressure system in basins with high geotemperature exhibits a kind of “non broken line mode” characterized by the straight line relation between geotemperature and geopressure of normal geotemperature—geopressure system in shallow layers and the exponential relation between geotemperature and geopressure of overpressure geotemperature—geopressure system in deep layers. In this mode the overpressure fluid in deep layers has stronger filling power both vertically and laterally so that oil and gas can migrate to relatively shallower and further traps for accumulation along faults, fractures and sand bodies. The model, that perfects the geotemperature—geopressure system concept, especially for the study of basin of high temperature of the oil and gas exploration, can greatly improve the oil and gas exploration potential.