According to the related concepts of cloud model and the limited interval theory, the comprehensive evaluation method based on combination weight and improved cloud model is adopted to solve the problems of single result of benefit evaluation, randomness and fuzziness of index evaluation of the Eastern Route of South-to-North Water TransferProject. The method combines the weight obtained by G1 and improved CRITIC weight method with the index membership degree obtained by the improved trapezoidal cloud model to realize the comprehensive evaluation of the project benefits. Taking the first phase of the Eastern Route of South-to-North Water Transfer Project in Jiangsu as an example, the influencing factors of project benefit evaluation were classified from cost analysis and benefit analysis, and the engineering benefit evaluation index system was constructed, including six aspects of fixed investment, annual operation cost, working capital, economic benefit, social benefit and ecological benefit, containing a total of 20 indexes with determined hierarchical standards. The effectiveness and applicability of the proposed evaluation system and method for the Eastern Route of South-to-North Water Transfer ProjectinJiangsu were verified.