Environmental vulnerability analysis is an important issue in conducting sustainable basin management. In our past study, we developed a set of criteria from three categories of factors (geographic, hydrologic, and societal) for assessing basin environmental vulnerability. According to a survey and the analytical hierarchy process (AHP) analysis, seven criteria were selected as a set of criteria, and the weights of these criteria were determined. This study adopts two different multiple criteria analysis (MCA) methods, the weighted method and the compromise method, to integrate the criteria and evaluate the environmental vulnerability of major basins in Taiwan. The results show that the Cho-Shui River Basin has the highest environmental vulnerability, no matter which method is used. However, the environmental vulnerability of the Ta-Chia River Basin is higher than that of the Tan-Shui River Basin and the Tseng-Wen River Basin when considering the measure of individual regret by the modified VIKOR method, which generates a different ranking than that of the weighted method. Stricter land-use restrictions should be placed on those basins that have higher environmental vulnerability. According to the analysis, the results of basin environmental vulnerability, land-use classification strategies can be created.