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Previous in situ observations have suggested that bottom water temperature variations in shelf seas can drive significant ocean bottom heat flux (BHF) by heat conduction. The BHF-driven bottom water temperature variations, however, have been overlooked in ocean general circulation models. In this study, we established a sea-sediment fully coupled model through incorporating the BHF. The coupled model included a sediment temperature module/model, and the BHF was calculated based on the sediment heat content variations. Meanwhile, we applied temporally varying BHF in the calculation of the bottom water temperature, which further determined the sediment temperature. The two-way coupled BHF process presents a more complete and physically reasonable heat budget in the ocean model and a synchronously varying sediment temperature profile. The coupled model was validated using a one-dimensional test case, and then it was applied in a domain covering the Bohai and Yellow Seas. The results suggest that when a strong thermocline exists, the BHF can change the bottom water temperature by more than 1°C because the effects of the BHF are limited to within a shallow bottom layer. However, when the water column is well mixed, the BHF changes the temperature of the entire water column, and the heat transported across the bottom boundary is ventilated to the atmosphere. Thus, the BHF has less effect on water temperature and may directly affect air–sea heat flux. The sea-sediment interactions dampen the amplitude of the bottom water temperature variations, which we propose calling the seabed dampening ocean heat content variation mechanism (SDH). [ABSTRACT FROM AUTHOR]