In order to explore the influence of wind load on the structure of Kezi River aqueduct, considering the economic cost and time cost, numerical simulation is used to study. Based on the CFD theory of fluid mechanics, this paper uses Midas NFX CFD software to study the wind field environment and wind load response of the Kezi River aqueduct, and simulates the influence of wind load on the aqueduct under different wind attack angles. By comparing with the existing wind tunnel test results, the reliability of the numerical simulation results is verified, and the influence of the change of wind attack angle on the aqueduct is deeply analyzed. The influence of the change of wind attack angle on the three-component force coefficient of the aqueduct is verified by the combination of numerical simulation and single factor variance analysis. The calculation results show that the wind attack angle has a significant effect on the three-component force coefficient, and the numerical simulation can quickly and efficiently simulate the complex wind field environment around the Kezi River aqueduct, and can intuitively reflect the distribution law of the negative pressure area on the surface of the aqueduct. The research results have certain reference significance for the structural design of the aqueduct wind load.