Water shortage, water pollution, shrinking water area and water mobility are the main contents of the water resources crisis, which are widespread in the social and economic development of Jilin Province. In this paper, a three-stage hybrid model integrating evaluation, prediction and regulation is constructed by combining the load-balance method and the system dynamics method. Using this model, the current states of water resources carrying capacity (WRCC) in 2017 and the trend of water demand/available from 2018 to 2030 were obtained. Using the orthogonal test method, the optimal combination program of agricultural and industrial water efficiency regulation and water resources allocation was selected. The results show that the pressure of the human–water resources system in Changchun, Liaoyuan and Baicheng is greater than the support, and the other six cities are not overloaded. The water demand in Jilin Province and its nine cities will increase from 2018 to 2030, if the current socio-economic development pattern is maintained. Therefore, we change the water quantity carrying capacity index by controlling agriculture, industrial water efficiency and trans-regional water transfer. Compared with 2015, among the optimal program obtained, the change range of the water use per 10,000 RMB of agricultural output is (−5%, 25%), and the water use per 10,000 RMB of industrial added value is (−45%, −35%), and the maximum water transfer is 1.5 billion m3 per year in 2030. This study analyzes the development pattern of WRCC in the process of water conservancy modernization in Jilin Province and provides reference for other provinces to make the similar plan.