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Water scarcity in China has long been discussed and studied, mostly in arid and semi-arid Northern China. However, temporary water scarcity caused by seasonal droughts hasn’t drawn enough attention still, while some humid regions in South China are readily to be encountered with seasonal droughts, especially in the background of climate change. In this study, a method based on System Dynamics (SD) and mathematical optimization is developed to analyze the situation of temporary water scarcity and optimize the water allocation under seasonal droughts, considering rapid urbanization, industrialization, and increasing food demand. And a case study in Nanchang Municipality, a typical humid region in Southern China, is presented. The simulation results show that conventional management scenarios including enforcing demand reduction strategies and increasing local water supply will not fill the water shortage gap, and the total water shortage rate will retain more than 9.0 % in special drought condition. Thus, we examine the water transfer scenario, and it proves to be effective in coping with the water shortage gap. The optimization results indicate that the water transferred from Ganjiang River to Fuhe River Water Demand Subsystem may account for 50.21 % of the total fresh water supply of Fuhe River Water Demand Subsystem, in September, under a certain drought condition. In addition, the current situation reveals fierce competition between social economic water needs and eco-environmental water requirements in local scale in dry condition. The situation argues that management of the distribution of water in space must be involved, and the simulation of the inter-basin transfer scenario proves it a necessary and effective countermeasure.