To solve the risk assessment problems of hydraulic engineering project construction, by considering the complexity of the interaction between indicators, the structural equation fuzzy evaluation model was used to evaluate the risks of hydraulic engineering projects, which was then applied to the construction stage of M reservoir project. It can be concluded that the level of risk assessment in the construction stage of the project was low, and the results of the model were consistent with those of the AHP fuzzy comprehensive evaluation, which was consistent with the level of risk of actual project. In addition, it is easy to determine the weight of indicators by using this model, and the covariance interaction coefficient between risk level indicators can be used to quantify the degree of interaction between indicators, thus improving the management level of hydraulic engineering projects. In conclusion, the application of structural equation fuzzy evaluation model to the risk study of hydraulic engineering project construction stage has certain potential, which is worth for further studies.