For the first time, the SCE-UA (Shuffling Complex Evolution-University of Arizona) method is used to solve the management model for deep groundwater resources of the Yangtze Delta, which is a multi-aquifer system with large area and complicated geology conditions. A series of environmental geology problem, such as decreasing of groundwater resources, the land interstice and the land subsidence, emerged as the result of long-term excessive exploitation of the groundwater resources in deep aquifers. The land subsidence is the most seriously one because it increased rapidly, effected on large area and resulted in huge hazards. Therefore, management model of groundwater resources in deep aquifers is built with the land subsidence taken into account. The management model is solved by the SCE-UA method and the GA (Genetic Algorithm) method respectively. Comparing the optimization results of thees two methods, we can see that the SCE-UA method was effectively used to solve management models of groundwater resources in multi-aquifer system with large area and complicated geology conditions. At the same time, the optimization results provide scientific basis for using groundwater resources in deep aquifers reasonably in the future.