A 3D thermal modelling within the northern North Sea and the adjacent land areas has been performed to reveal time-dependent changes of the subsurface 3D thermal pattern during Cenozoic erosion and deposition. The results of the 3D thermal modelling provide significant progress in our understanding of the first-order characteristics of the conductive thermal field within the northern North Sea and adjacent land areas. The obtained results of the transient 3D thermal simulations clearly indicate that the present-day subsurface thermal field is non-equilibrated within the areas where Cenozoic erosion and deposition have taken place. The obtained erosion-related positive thermal anomaly reaches its maximum of more than + 33°C at a depth range of 18–26 km beneath the continent and adjacent shelf areas where the thickness of the eroded material is the largest. The deposition-related negative thermal anomaly is around - 34°C at 22–26 km depths beneath the Central Graben, where the Cenozoic sequence is thickest. The thermal effects of erosion and deposition within the study area are caused by the heat advection by heated or cooled solid rocks as a result of vertical upward or downward movements of these rocks. Besides, the hypothetical deep tectonics-related heating events could have occurred during the Cenozoic within the central part of the North Sea.