Surface Heat flow (HF) can be calculated from the accumulation of radiogenic heat production (RHP) of arbitrarily subdivided thin layers of the crust and the residual HF. However, geothermal studies of scientific drilling projects around the world do not have clear vertical correspondence between HF and RHP, which has created a great controversy for the relationship between the two. For the first time, continuous temperature data, thermal conductivity and RHP measurements from the 3,008‐m‐deep Lujiang‐Zongyang Scientific Drilling in the northeastern Yangtze Craton, demonstrate that the abnormal HF is determined by high RHP rock (mean value, 10 μW/m3). The detailed spatial‐temporal study of magmatic activity in the Lujiang‐Zongyang basin shows the high RHP rock are concentrated in the early syenite‐monzonite period (133–131 Ma) in the northern basin. Two enrichment processes caused by late Neoproterozoic and Mesozoic subduction contribute to the formation. Plain Language Summary Heat flow (HF) is the most important parameter to characterize the thermal state of the Earth's interior. The surface HF can be calculated from the accumulation of heat production of subdivided thin layers of the crust and residual HF. However, no direct evidence of HF and heat production vertical variation has been found in the present continental scientific drilling wells. In this study, the contribution of the vertical variation of heat production to the surface HF is confirmed for the first time, and the HF values significantly higher than the regional background are determined by the high heat production rock. The study of the genesis of the high heat production rock concluded that they likely underwent two enrichment processes in the Late Neoproterozoic and Mesozoic, respectively, with the Late Mesozoic enrichment process being completed in a very short period of time. Key Points First direct evidence was found to confirm that surface heat flow is determined by the heat production The relationship between natural gamma‐ray and heat production is reconstructed The formation of rocks with high heat production result from two enrichment processes