Water resources optimal allocation is an effective way to solve water shortage and has important significance for the sustainable development of regional socio-economy. The optimal allocation model of water resources is a complex comprehensive system. It is difficult to find the global optimal solution using the traditional optimum method. The non-dominated sorting genetic algorithm(NSGA-Ⅱ) is one of the most effective methods to solve multi-objective optimal problems. However, there is little application in the field of water resources optimal allocation. Taking the Chanba River basin for example, the paper used NSGA-Ⅱ to set up the model of multi-objective water resources optimal allocation and study the applicability of the method in the model solution of water resources optimal allocation. The results of water resources allocation gotten by the method are reasonable and applicable.