According to the imbalance development and utilization of water resources, water shortages and other issues in Sanjiang Plain, taking Jiansanjiang branch bureau as an example, the multi-objective optimal allocation model of water resources is established with goal of maximum economic and social benefits. Only surface water, groundwater and transit water are considered overall and different water demands in industry, life and agriculture are satisfied can we realize the rational allocation of regional water resources. The large system decomposition-coordination theory and multi-objective genetic algorithm are applied to solve the model. The optimization results showed that, the water shortage situation in Jiansanjiang branch bureau is improved in planning years and surface water supply capacity can be increased gradually and groundwater resources can be effectively protected. The optimal allocation model and solution method are effective and feasible, and the optimal allocation results are reasonable. The research can provide scientific basis for rational development and utilization of water resources in Jiansanjiang branch bureau and Sanjiang Plain.