Integration of the food, energy, and water (FEW) nexus thinking is expected to enhance cross-sectoral discussion during the process of policy development. This process can be improved with comprehensive assessment tools to provide quantitative information regarding the interdependence of the FEW nexus. A comprehensive framework of the regional FEW nexus quantitative assessment was proposed in this study. Life cycle assessment (LCA) was the core method used to evaluate the FEW inter-linkages. Land use data which can further imply the resources consumption or requirement was introduced to estimate potential changes in the nexus in future time periods. In order to display the practicality of the FEW nexus approach, a user-friendly nexus platform, a GIS-based Regional Environmental Assessment Tool for Food-Energy-Water nexus (GREAT for FEW) (http://greatforfew.enve.ntu.edu.tw/FEW/), was developed with a solid conceptual model, a database, and calculation methods. The usability of the tool was demonstrated using a Taiwanese case study. The results of the Taiwanese case showed that Scenario 1 (non-nuclear homeland policy) caused the lowest environmental impacts as compared to both Scenario 0 (baseline) and Scenario 2 (non-nuclear homeland policy with National Spatial Plan) due to better energy structures and maintenance of agricultural lands. These outcomes indicate that the selection of indicators does affect the results. Therefore, it is suggested that additional indicators should be designed based on the characteristics of the case study area and concerns of stakeholders.