The Pearl River Mouth Basin (PRMB) is located on the northern margin of the South China Sea (SCS). Heat flow measurements indicate that the PRMB is a typical ‘hot basin' characterized by a high background heat flow. However, the tectono-thermal evolution of the PRMB and the mechanisms involved are still controversial due to the different input parameters used in tectono-thermal models, small datasets and the limited area of the basin studied. We used tectono-thermal modelling with a multi-stage finite stretching model, constrained by extensive well data, to systematically analyse the tectono-thermal evolution of the PRMB since the onset of rifting. The study area was expanded relative to previous studies to cover both the proximal and hyperextended regions of the northern SCS margin, providing a more comprehensive understanding of its tectono-thermal history. Numerous wells and seismic data covering the entire basin were used, along with appropriate input parameters, to address the gaps in previous studies and to enhance the accuracy of the results. Our findings indicate that the PRMB underwent two phases of heating, primarily due to thinning caused by lithospheric extension during rifting. By the end of rifting, the Northern Depression Zone and the Kaiping Sag had reached peak heat flow, while the Panyu Lower Uplift and Baiyun Sag saw their highest heat flow since the initial rifting. The PRMB experienced thermal decay during the post-rift stage, but a significant reheating event occurred from 23.03 to 13.82 Ma, likely due to northwards lower crustal flow from the Baiyun Sag. The Panyu Lower Uplift and the Baiyun Sag had reached their peak heat flow by 13.82 Ma and the heat flow generally increased by 1–3 mW m −2 in the other studied areas during this stage. The basin's thermal decay slowed at 5.33 Ma and localized heating events linked to magmatic activities in the southern Dongsha Uplift were observed. In general, the proximal domain of the northern SCS margin reached peak heat flow by the end of rifting, whereas the hyperextended domain reached peak heat flow by 13.82 Ma. The heat flow in the hyperextended domain was generally higher than that in the proximal domain as a result of the thinner crust of the hyperextended domain caused by intense multiple lithospheric detachment–extensional thinning processes. During the rifting stage, the lithospheric extensional thinning process was the most important factor influencing the tectono-thermal evolution of the northern SCS margin, while lower crustal flow and magmatism were the most important factors during the post-rift stage.