Dike engineering is the most effective method for flood prevention. Considering the ecological problems brought by dike construction, it is of great significance to establish an ecological destruction evaluation model in the dike interference area. To solve the uncertainty of the ecological destruction evaluation in dike interference area, triangular fuzzy numbers are introduced into the set pair analysis, so as to obtain the ecological health evaluation level and ecological destruction degree. The application in Amur River validates the validity of the model. This model can provide basis for ecological restoration and dike engineering management.