This research aims to identify several decision-making gaps which seem to be existed around Food-Energy-Water Nexus through local case study in the Kyoto city, Japan. Our research methodologies include calculating food self-sufficiency ratio at local level using national statistics, production area proportion of each food categories using local market reports, and conducting impact assessment for Water-Energy Nexus based on several scenarios of food policy. Based on the above calculation and scenario analysis on several food policies, decision-making gaps regarding Food-Energy-Water Nexus is abstracted. During the scenario analysis, decision-making gaps regarding Food-Energy-Water Nexus are found. In other words, while a watershed is decided automatically by natural and geographical conditions, energy-shed usually depend on big electricity companies and food-shed consists of consumers’ preferences, retailers’ procurement policy, farmers’ tendency to change (or not change) their production style and so on.