Evaluation of the regional sustainable use of water resources (SUWR) is one of the core issues for studying regional sustainable development strategy. In the process of evaluation, it is crucial to select a reasonable and applicable evaluation methods to improve the reliability of evaluation results. In this paper, the index system of SUWR was established by coupling eco-environment, socioeconomic and water utilization system. The dipartite degree theory (DD) and the serial number synthesis theory (SNS) were applied for selecting the suitable sustainability assessment method among six evaluation methods. The selected method was used for analyzing the spatial difference in Fujian Province, China. Results indicated that (1) based on different evaluation methods for the SUWR, the stability and reliability of fuzzy matter-element analysis are higher than those of fuzzy comprehensive evaluation, attribute recognition, improved rank correlation, principal component analysis and grey relation analysis; (2) The regions with a higher level of SUWR are concentrated in the west of the research area, while the eastern regions have a lower level. The highest sustainable level of water resources was 0.647, in Longyan city and the lowest level was 0.399, in Xiamen city; (3) The superimposition effects of water resource conditions, topography and economic development level formed the spatial distribution pattern of sustainable utilization level. The results may provide scientific guidance for the effective evaluation of regional SUWR, water resources management and government decision-making.