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Abstract 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.