Inter-basin Water Transfer Projects require the appropriate financing model to attract large amounts of social investment. Therefore, financing model decision becomes the key of engineering construction. In three aspects, such as the subject, the object and the target of the financing model, Grey Target Model is established in this paper. First, the complex financing mode decision problems of Inter-basin Water Transfer Projects are decomposed by using hierarchical decomposition method. Then Analytical Hierarchy Process (AHP) method is used to calculate the comprehensive weight of evaluation index. Experts’ opinions financing model are transformed into the evaluation matrix based on the Dephi method. The Weighted Grey Target Model is used to calculate the approaching degree of financing model and assists financing mode decision. In addition, this paper takes the water diversion project from the Han to the Wei River of Shaanxi Province as a verification example for the model. For other water diversion projects, the evaluation results are also reliable and provide theoretical references for the financing model decision of Inter-basin Water Transfer Projects.