The food-energy-water nexus (F-E-W) serves as a crucial resource for the sustainability of households, while the efficiency of resource use largely depends on our understanding and management of the nexus including all three factors. Limited research has been conducted on this topic thus far because of the increasing complexity of home technologies and data availability. This study develops an evidence-based system dynamics model for assessing the synergy and trade-offs of the household F-E-W. By applying the system dynamics (SD) methodology, the FEW consumption and generation originating from home appliances were modelled and simulated. The model was applied to an eco-house in Tokyo, and its efficacy was validated with one-year hour-based observations of a home energy management system (HEMS). The findings revealed that water-related and food-related energy use accounted for approximately 55% of the total energy use. In addition, water-related energy use showed high uncertainty, suggesting a management potential of approximately 24% for reduction, and was significantly correlated with household carbon emissions. Moreover, this result verified that the effective management of household energy consumption requires the adept manipulation of the diverse array of energy sources employed for air and water heating, while HEMSs could play a key role in implementation.