At present, global water resource security is facing serious threats, and the construction of a cooperative, open, and mutually beneficial water resource community is a potential solution to the global water resource crisis and water resource hegemony. Previous studies on the formation and beneficial distribution of water resources in cooperative alliances have more often focused on the idea that participants take all of their water resources when they join a cooperative alliance (i.e., a crisp cooperative alliance), while fewer studies have focused on participants including different proportions of their water resources and joining multiple cooperative alliances (i.e., fuzzy cooperative alliances), and even fewer comparative studies concern the use of different benefit-sharing mechanisms. In this paper, in order to improve the efficiency of water use, allocate water resources more optimally, and generate higher returns for water users in a given basin, we propose the establishment of a traditional crisp and improved fuzzy cooperative alliance for water resources in the basin from the perspective of cooperative game theory; we examine the water resource allocation mechanism within the alliance based on the principle of priority; we construct a benefit allocation mechanism for the cooperative alliance based on the core, least core, weak least core, and Shapley value method; and we carry out empirical research using the example of the Tarim River Basin. Our findings are as follows: (1) A cooperative alliance based on the perspective of cooperative game theory can effectively improve overall benefits and individual benefits, and a fuzzy cooperative alliance is more effective than a crisp cooperative alliance in improving the overall water benefits of the region. (2) The participants in the fuzzy cooperative alliance can obtain more benefits than in the crisp cooperative alliance, and the benefit distribution mechanism of the cooperative alliance helps the participants to determine the object of cooperation while maintaining the sustainable existence of the alliance. (3) The different methods of benefit distribution within the cooperative alliance directly affect the overall water benefits of the region. (4) The different methods of benefit distribution directly affect the stability of the alliance, and the players in the game have heterogeneous preferences for different distribution schemes. The resource-sharing mechanism and benefit distribution mechanism of a water resource cooperative alliance have good applicability as solutions to the problem of water resource optimization and allocation in river basins, and they may provide policy references for the efficient use of water resources and optimization of water resource allocation and management in areas with a shortage of water resources, such as arid and semi-arid zones.