There are some factors,such as the topographic relief,sedimentary thickness and thermal conductivity, magmatic activity and thermal cooling,influencing the seafloor heat flow and the evolution of lithosphere structure in southwest sub-basin(SWSB),South China Sea.On the base of the geological structure characteristic of SWSB this paper will discuss some other factors including thermal anomaly area,dike produced by magma intrusion and lithosphere relief,by modeling and calculating.Calculating results indicate partial areas where temperature is higher than vicinity in the lithosphere,which we call thermal anomaly here containing thermal anomaly area and dike in this paper,could decrease heat flow below,increase above,and gradually increase to two sides;heat flow in upwelling parts of lithosphere is usually higher than sinking parts,and in the middle is of a gradual transition. There are some factors, such as the topographic relief, sedimentary thickness and thermal conductivity, magmatic activity and thermal cooling, influencing the seafloor heat flow and the evolution of lithosphere structure in southwest sub-basin (SWSB), South China Sea. On the base of the geological structure characteristic of SWSB this paper will discuss some other factors including thermal anomaly area, dike produced by magma intrusion and lithosphere relief, by modeling and calculating. Calculating results in partial areas where temperature is higher than vicinity in the lithosphere, which we call thermal anomaly here containing thermal anomaly area and dike in this paper, could not decrease heat flow below, increase above, and gradually increase to two sides; heat flow in upwelling parts of, and in the middle is of a gradual transition.