The establishment of an evaluation index system for performance of optimal allocation of water resources comprehensively considering the economic, social and water environmental goals is in favor of providing the relevant institutional guarantee for implementing the River Chief System in China. According to the principle of the corresponding evaluation indices required by the goals, a multi-layered evaluation index system including economic development indices and public demand satisfaction indices, which covers economic rationality, social rationality and ecological rationality, is proposed by discussing the allocation of water resources reflected in the new development concept. The evaluation index system is composed of 5 indices of the economic cost, economic benefit, water consumption for daily life, water ecological environment index and industrial safety index and some sub-indices. Their weights can be calculated level by level by the group decision eigenvalue method done by some experts.