A general framework for the analysis of the urban water-energy nexus (WEN) was proposed and a dynamic and quantitative WEN model was developed based on the Long-range Energy Alternatives Planning System (LEAP) and Water Evaluation and Planning (WEAP) tools. Using Xiamen, China, as a case study, eleven future scenarios were designed to explore the impacts of different factors, from both supply and demand sides, on urban WEN. Both water-related energy (WRE) and energy-related water (ERW) were studied to reveal the interconnected relationship between water and energy. We found that most WRE and ERW savings lie on the supply side, except for demand management scenarios, and most scenarios have larger trans-boundary effects than in-boundary effects due to the import of large quantities of energy and water. Industry structure adjustments (oriented toward energy or water savings) and energy-saving measures have better co-benefits in terms of energy and water savings than other measures. Promoting electric vehicles increases electricity imports and related trans-boundary ERW. Such effects should be considered before importing resources from outside city boundaries. Developing high-tech industries might also increase energy or water burdens. Finally, the boundaries of urban WEN research were discussed to promote additional comparable studies.