The rapid growth of tourism economy in Beijing has intensified the consumption of resources and the pollution of the environment, and the coupled relationship among food, energy, and water requires rigorous research and discussion. This study developed an environmental extended input-output model by combining 42 sectoral input-output tables and tourism statistics in Beijing. It also carried out the food-energy-water (F-E-W) accounting and evaluation of the tourism industry. Then, through structural decomposition driving force analysis, it proposed a synergistic F-E-W reduction strategy for the tourism industry in Beijing. Results of the study show that the F-E-W related sectors consume a total of 605.6 million m³ of water and 21.1 million tons coal equivalent (tce) of energy to sustain the operation of the tourism industry in Beijing; the food supply group generates the largest tourism water footprint, accounting for 72.1%. The tourism direct group generates the largest tourism energy footprint, accounting for 58.3%; and the food and water supply groups are the key contributors to the F-E-W correlation. From 2012 to 2017, Beijing’s tourism water footprint (TWF) decreased by 46.3%, and tourism energy footprint (TEF) increased by 23.7%. Structural decomposition analysis shows that the reduction in Beijing’s TWF is driven by the changes in production structure. Conversely, the increase in TEF is driven by scale effects. Through eco-innovation of tourism enterprises, government environmental regulation of tourism and guiding travelers to green consumption can promote synergistic F-E-W emission reduction.