To determine the key influence factors of chlorophyll-a (Chl.a) in the Lake Hanfeng, water temperature (T), pH, Chl.a, Secchi depth (SD), and nitrogen (N) and phosphorus (P) nutrients in Lake Hanfeng in the Three Gorges Reservoir from 2018 to 2021 were analyzed, and the correlation between Chl.a and other water quality indicators was revealed, and the key influencing factors of Chl.a were analyzed by the structural equation model. The results showed that Chl.a in Lake Hanfeng T ranged from 0.04 to 68.58 μg/L, and T ranged from 9.62 to 32.10℃, pH ranged from 6.75 to 9.81. Total nitrogen (TN), dissolved nitrogen (DN), total phosphorus (TP) and dissolved phosphorus (DP) in the Lake Hanfeng varied from 0.58 to 4.68, 0.25 to 3.99, 0.02 to 0.76 and 0.01 to 0.44 mg/L. Chl.a concentration was positively correlated with T, pH, TP and total suspended solids. Conversely, Chl.a concentration was negatively correlated with alkalinity, DN, nitrate nitrogen, nitrite nitrogen and SD. The structural equation model results showed that the path coefficient of physical factor in the factors affecting Chl.a concentration was 0.68 and nutrients 0.16, indicating that the factors affecting Chl.a concentration were mainly physical factor and the nutrients were less important. Meanwhile, physical factor indirectly affected Chl.a concentration through nutrient salts (path coefficient is -0.04). In each physical factor, the path coefficient of T and pH was 0.51 and 0.41, respectively, while T was the main characterization index of the physical factor; the path coefficients of TP and DP were 0.82 and 0.71, respectively, while the path coefficient of TN was 0.36 and P was a limiting nutrient element of Lake Hanfeng.