Abstract: The seafloor heat flow, as an effective parameter to the study of thermal state, is an important indicator of the oceanic crust or upper crustal lithosphere. To understand the geothermal distribution pattern of the deepwater areas of the South China Sea, the geothermal data of IODP Expedition 349 is processed and studied. We acquired shallow thermal conductivities at four sites and seafloor heat flow data at three sites. The results show that the thermal conductivity varies in a range of 0.8 ~ 2.2W/(m·K), which depends upon the composition of sediments. The thermal conductivity of the sediments increases slightly with depth, probably owing to the effect of sediment compaction. The heat flow of Hole U1431D, Hole U1432C and Hole U1433A is 24±8mW/m², 105±3mW/m² and 89±2mW/m² respectively, basically consistent with previous results and the data from the nearby area. It proves that our results are reliable. The reverse of geothermal gradient and the low heat flow at Site U1431 might be caused by a downwell limb of hydro-thermal circulation.