ObjectiveTo identify the major ecological drivers for malaria vector density using the structural equation model (SEM) in the Three Gorges Reservoir.MethodAn 11-year longitudinal surveillance of malaria vector as well as its related ecological factors was carried out in the Three Gorges Reservoir. The Delphi method was used to identify associated ecological factors. The structural equation model was repeatedly corrected and improved by the corrected index, combined with the actual situation. The final model was defined by relative simplicity, best fitting as well as the practicality.ResultThe final model indicated that the direct effects of temperature, livestock, humidity, and breeding on the vector were 0.015, −0.228, 0.450, 0.516 respectively, their total effects on the vector were 0.359, −0.112, 0.850, and 0.043 through different pathways.ConclusionSEM was effective and convenient in elucidating the mechanism by which malaria vector dynamics operated in this study. It identified that the breeding had the highest direct effect on vector and played a key role for mediating effect of temperature and humidity.