In order to reduce the subjective influence imposed by indicator selection and weight determination, the method coupling rough set and catastrophe progression has been proposed for the comprehensive sustainable utilization evaluation of regional water resources. Taking nine cities of Fujian Province as basic research units, an evaluation index system consisting of four criteria and twenty indicators is constructed to evaluate the sustainability of water resources. The results show that the method of coupling rough set with catastrophe progression is feasible in evaluating the sustainability of water resources, due to its superiority of screening redundant information and reducing the subjective influence imposed by human intervention. The sustainability of water resources utilization in Fujian Province is in a descending order as follows: Longyan, Sanming, Ningde, Nanping, Zhangzhou, Fuzhou, Quanzhou, Putian and Xiamen, showing a declining trend from the northwest toward the southeast. Based on the evaluation results, nine districts and cities can be divided into four partitions, providing a theoretical basis for the exploration, utilization and protection of water resources in Fujian Province.