The Qiongdongnan Basin (QDNB) and Pearl River Mouth Basin (PRMB) are located in the northern continental margin of South China Sea. Based on the data from 13 seismic lines, tectonic and thermal modeling were performed in order to study the tectonic and thermal history in the northern South China Sea during the Cenozoic era. The results show that the PRMB experienced two episodes of heat flow rising processes. The first episode occurred from 56.5 Ma to 32 Ma, and the second one occurred from 32 Ma to 23.3 Ma. The QDNB experienced three episodes of heat flow rising processes and two episodes of cooling processes.