An evaluation index system of water resources ecological-economic sustainable development in the Yellow River Basin including 13 indexes was established based on Emergy theory in ecological economics with water resources ecological-economic system being seen as an organic whole from four aspects of the system energy flow, economic development energy, water resources energy and sustainable development energy of river basin. The development and utilization of water resources, economic development and sustainable development of water resources ecological-economic system in every province along the Yellow River Basin were evaluated. The results show that the Yellow River Basin belongs to the consumptive ecological-economic model. The socio-economic development and modernization degree of the upper reaches of the Yellow River are lower than those of the lower reaches of the Yellow River. The energy use intensity of water resources in the Yellow River Basin matches the level of economic development while doesnt match the contribution rate of water resources to the social and economic system, which implies that the allocation of water resources should be further optimized. The environmental pressure in the Yellow River Basin is huge and the level of sustainable development is low. It is necessary to increase the investment of renewable resources to realize the sustainable development of the system.