The characteristics of thermal density flow in tributary reservoirs are an important basis for studying the mechanism of algal blooms. The density difference caused by water temperature difference between the mainstream reservoir and the tributary bay leads the mainstream of the Yangtze River flows into the tributary bay through the middle layer, surface layer and bottom layer in spring-summer, autumn and winter, respectively. The normal operation of the Three Gorges Reservoir goes through four stages every year: pre-flood drawdown season, flood season, post-flood storage season and dry season, with a maximum daily water level fluctuation of 3.0 m/d. Based on the calibrated and verified three-dimensional hydrodynamic and water temperature mathematical model of the Xiangxi Bay, different water level fluctuation conditions were simulated to analyze the characteristics of thermal density flow. The results show that with the water level rises, the backflow velocity and backflow thickness of the mainstream of the Yangtze River increase, while the inflow velocity of the upstream decreases. With the water level drops, the backflow velocity and backflow thickness of the mainstream of the Yangtze River decrease, while the inflow velocity of the upstream increases. The greater the daily increase of water level, the greater the backflow distance of the density flow from the mainstream of the Yangtze River. The greater the daily decrease of water level, the much smaller the backflow distance of the density flow from the mainstream of the Yangtze River. The maximum decline of the backflow distance from the mainstream of the Yangtze River is 40 percent with the daily water level decrease of 2.0 m/d. Cyclical water level fluctuation can cause cyclical water flow in tributary reservoirs. A high frequency of water level fluctuations (1.0 m every 6 hours) forces the mainstream reservoir and the tributary bay to be completely mixed in the middle and lower reaches of the tributary bay, which would reduce hydraulic residence time and limit the growth and aggregation of algae. Short-term (≤4 d) and small-amplitude (≤2.0 m/d) water level fluctuations are difficult to change the stable water temperature stratification state of the Xiangxi Bay, and the average depth of the thermocline does not exceed 5.0 m.