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Under the combined impacts of climate change and human activities, a series of water issues, such as water shortages, have arisen all over the world. According to current studies in Science and Nature, water security has become a frontier critical topic. Water supply security (WSS), which is the state of water resources and their capacity and their capacity to meet the demand of water users by water supply systems, is an important part of water security. Currently, WSS is affected by the amount of water resources, water supply projects, water quality and water management. Water shortages have also led to water supply insecurity. WSS is now evaluated based on the balance of the supply and demand under a single water resources condition without considering the dynamics of the varying conditions of water resources each year. This paper developed an optimal allocation model for water resources that can realize the optimal allocation of regional water resources and comprehensively evaluate WSS. The objective of this model is to minimize the duration of water shortages in the long term, as characterized by the Water Supply Security Index (WSSI), which is the assessment value of WSS, a larger WSSI value indicates better results. In addition, the simulation results of the model can determine the change process and dynamic evolution of the WSS. Quanzhou, a city in China with serious water shortage problems, was selected as a case study. The allocation results of the current year and target year of planning demonstrated that the level of regional comprehensive WSS was significantly influenced by the capacity of water supply projects and the conditions of the natural water resources. The varying conditions of the water resources allocation results in the same year demonstrated that the allocation results and WSSI were significantly affected by reductions in precipitation, decreases in the water yield coefficient, and changes in the underlying surface.