The characteristics of thermal density flow in tributary reservoirs are an important basis for understanding 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 flow into the tributary bay via the middle layer in spring-summer, surface layer in autumn and bottom layer in winter. 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 maximum daily water level fluctuations reaching up to 3.0 m/d. Based on a calibrated and validated three-dimensional hydrodynamic and thermal model of Xiangxi Bay, we simulated various water level fluctuation scenarios to analyze the characteristics of thermal density flow. Results show that with the rising water level, 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 drop, 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 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 reaches 40% with the daily water level decrease of 2.0 m/d. Cyclical water level fluctuation can cause cyclical water flow in tributary reservoirs. High-frequency fluctuations of water level (1.0 m every 6 hours) can induce completely mixing between the mainstream reservoir and the tributary bay in the middle and lower reaches, thereby reducing hydraulic residence time and limiting the algal growth and aggregation. Short-term (≤4 d) and small-amplitude (≤2.0 m/d) water level fluctuations are insufficient to disrupt the stable thermal stratification of Xiangxi Bay, where the average thermocline depth remains below 5.0 m.