With rapid development of society and economy, the issue of water shortage has presently been more and more serious in China. Optimal water and land resources allocation, involving many aspects such as society, economy, ecology etc., is a rational approach to solve this problem. In this study, a substantially improved model, i.e., multi-objective optimal allocation, is established for coordinating the usage of water and land resources. The model was developed on the basis of Immune Genetic Algorithms (IGA), and it mainly includes three objectives and seven constraints. The results of case study show that there is no water shortage in the predicting year of 2020 in Dongtai City, Jiangsu Province by using the optimal allocation of water and land resources. The new optimal allocation proposed in this study has a positive influence to promote the economic and social harmonious development and the natural environment protection for coastal areas of China.