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Graphical abstract Highlights • The present-day heat flow increases from the north to south of the northern South China Sea. • In the continental shelf, heat flow increased rapidly twice during the Paleogene syn-rift stage, and followed by continuous thermal subsidence with heat flowdecreased during the Neogene post-rift stage. • The heat flow in the slope continuously increased due to multi-episode seafloor spreading, and gradually reduced after the cessation of the sea floor spreading. • The thermal evolution of the Pearl River Mouth Basin is mainly controlled by tectonic activities. Abstract The Pearl River Mouth Basin (PRMB), the largest basin in the northern continental margin of the South China Sea (SCS), has been one of the key areas to characterize geothermal field and thermal evolution of a passive continental margin. The thermal history of the Pearl River Mouth Basin is related to the seafloor spreading of the SCS in the late Early Oligocene. Heat flow measurements show that the PRMB is characterized by a high background heat flow with average heat flow of 71.8 ± 13.6 mW/m2. The present-day heat flow of the northern SCS increases from the northern shelf with the thick crust to the southern slope with the thinned crust. This study employs forward and inverse modeling to simulate the rift and post-rift processes exampled by four wells at different structural settings. Two thermal evolution models of the PRMB are established for continental shelf and continental slope. In the continental shelf, heat flow increased rapidly twice during the syn-rift stage, and then followed by continuous thermal subsidence with heat flow value decreased during the post-rift stage. While the heat flow in the slope continuously increased due to lithospheric thinning, mantle upwelling and resulting multi-episode seafloor spreading in SCS during the Neogene post-rift stage, which is different from the previously proposed decreasing heat model for the slope during the post-rift. Heat flow gradually reduced after the cessation of the sea floor spreading (10 Ma). The local multi-staged magmatic activities mainly contribute to the high level of maturity in the Liwan Sag located in the lower slope. [ABSTRACT FROM AUTHOR]