The optimal allocation of water resource is key to the sustainable development. By the qualitative analysis of the water shortages in Sanjiang plain due to hanging pump and local over-exploitation, a multi-objective water resource allocation model was set up based on the properties of water resource system with diverse targets. At the same time, paralleling choice GA with intrinsic parallelism and the ability of global search has been introduced to obtain a solution. Meanwhile, in order to realize the maximization of the comprehensive benefit in life, production and ecology, each calculation is converted into a unified economic benefit as a benchmark. The result showed that the combination of the model and the algorithm has optimized water resource use.