The Hani Rice Terraces represents a typical model of mountain agriculture and is successfully listed in UNESCO World Culture Heritage and the FAO Global Important Agricultural Heritage Systems due to their long history and effect on the cultural landscape. A number of previous studies showed that the success of the Hani Rice Terraces agro-ecosystem lies in the effective management of its water resources. However, there has not been a composite analysis of the institutional construction and ecological cultural connotations of water resource management in the Hani Rice Terraces agro-ecosystem. Based on an ethnoecological perspective, we undertook an analysis that combined the theories and methods of ecology and ethnology, etc. The results indicated that a water resource management system consisting of two core elements:conservation and distribution of the water resource, was key to solving the temporal and spatially uneven distribution of the water resource. Furthermore, an ecological culture institution supported by migration culture, religious culture, customary law, and traditional knowledge revealed the ecological cultural connotation that guaranteed the building and implementation of a management system for the water resource. This study can provide valuable experience on how to adapt to climate change, to promote the sustainable development of agriculture in other areas, and to improve theoretical water resources management systems in China.