Abstract: Based on the genetic algorithm and weight coefficient method, the joint allocation model of multi-water sources in Xiamen City is constructed by taking into account of multiple water sources such as surface water and groundwater, as well as constraints including water supply capacity and the supply-demand relationship. The optimization of multi-water source joint allocation in various administrative districts with economic, social, and ecological objectives is studied. The results show that only the scheme giving priority to social benefit can achieve higher guarantee rate of domestic water in extra-dry year. Under the conventional condition of groundwater exploitation, Siming district and Huli district inside the island are mainly allocated with the external diversion water from Jiulong River, while the other four districts outside the island are mainly allocated with local surface water and groundwater. Mining groundwater storage resources as emergency water source can greatly improve the water supply security, but also change supply structure in each district with a great increase of groundwater supply proportion. The results show that the genetic algorithm can be employed to rationally allocate various water sources with different objectives, and groundwater may play a greater role in ensuring water supply security.