The water competitions between human and nature pose a health problem of the water ecosystem. The relationship and health level of a water ecosystem, which are an important basis, are explored to formulate the sustainable development strategy of human society and natural ecology. The study proposes a new water ecology emergy (WEE) analytic system that comprises five main components: input module, storage module, output module, addition module, and consumption module. Based on the emergy theory, we have realized the quantification of ecological-economic flow inside and outside each module and converted each energy to emergy. Given this, the WEE analytic system health diagnosis indicators are proposed, including emergy interaction ratio, economic-social benefit ratio, ecological-environmental benefit ratio, water resource value, and sustainable development indicator. The comprehensive diagnosis method is the minimum information entropy (MIE) combination weighting method based on entropy and variation coefficient, which can comprehensively diagnose the health level of the system. Taking Luoyang, China as an example, the results show that for the WEE analytic system, the input module, output module, storage module, and consumption module were deteriorating, and only the addition module had a good trend. The health diagnosis results also show that the health level decreased year by year in the initial stage (2010–2015) and fluctuated and increased in the later stage (2015–2019). The main reason for the improvement of the system health level is the increase in the ecological-environmental benefit ratio. Harmonious development of human society and natural ecology, which consider the dual objectives of ecological-environmental protection and economic-social development, realize the benign operation of the water ecosystem and the sustainable utilization of water resources.