Abstract. Sustainable development in water resources is becoming a hot topic in recent years. The world is facing the disequilibrium between the availability of resources and the increase in population with fast-growing economies and social development. This study proposes a new methodological framework of sustainable development of water resources based on the response linkages and feedback loops of economy-ecology-food (EEF) nexus. It provides a new way to identify the interconnection and coevolution process between these EEF. The multi-objective model and system dynamic (SD) model were coupled to characterize the interconnections between processes and their dynamic responses to a set of scenarios. The combination of decomposition-coordination method (DC) and dynamic programming was used to find the optimal scenario based on each component of the EEF nexus. The Upper reach of Guijiang River Basin (UGRB) was presented as a case study. Results showed that the coupled multi-objective model and SD model presented in this study are able to characterize the interactions and feedback between EEF systems adequately. Most importantly, the rapid growth rate of socio-economic indexes will drive the awareness of river ecology and showed a higher sensitivity under different decision preferences. The results provided in this study can provide baseline information for stakeholders and policymakers in the field of water management for a better understanding of the interactions across systems.