To promote the harmonious development of human and water resources, the scarcity and ecological value of water resources should be considered in water resource allocation. In this paper, synergetic theory was applied to the process of water resource allocation, and we constructed a synergetic theory-based water resource allocation model by investigating the synergetic principle of each link of water resource allocation. The objective equation was established for determining the optimal comprehensive benefit of the composite system. Multidimensional constraint conditions were constructed from the perspective of the social benefit, economic benefit and ecological benefit of water supply, and balance equations were established. Order parameters were selected for the social, economic and ecological subsystems, and the order degrees of the three subsystems and the synergetic degrees of allocation schemes were calculated by using the fuzzy mathematics method to provide a basis for the recommendation of an optimal scheme. Finally, we proposed a multicycle iterative algorithm to realize the overall objective of “harmonious development between humans and water resources”, which provides an effective calculation tool for water resource synergetic allocation. This model was applied in Jilin, and an optimal scheme was recommended on the basis of a synergetic degree analysis, which shows that the water supply of conventional water sources will be saved by an increase in the reclaimed water supply. In addition, after the implementation of an external diversion project by 2030, the amount of groundwater withdrawal will be gradually reduced, and the water deficit rate will be significantly reduced.