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Reservoir regulation and local climate both affect the heat budget of tributary bay. It is difficult for traditional methods to identify the influence of different factors on heat budget quantitatively. In this paper, for analysis of the control mechanisms of the heat budget of a large reservoir tributary, the water temperature distribution, and heat budget processes of the Meixi River, a typical tributary to the Three Gorges Reservoir was measured, and a new method was used to calculate the heat content composition of the tributary bay and identify the key factor of the heat balance. The result shows significant variation in the spatial and temporal distributions of water temperatures in the Meixi River, ranging from 12.4 to 28.9 °C on the surface and 12.0 to 24.4 °C at the bottom. The total heat exchange across the air–water interface that ranges from 0.1 to 6% of the budget is not the primary control factor of the annual tributary heat budget. Rather, the change in water depth produced by regulation of the Three Gorges Reservoir is the primary control factor of the tributary heat budget in the whole year, which ranges from 72 to 99% of the budget. The water temperature difference between the main stream and tributary is the not key factor of the heat budget, which ranges from 0.1 to 28% of the heat budget.