Abstract: As a complicate ecosystem, the Yangtze River includes numerous organisms and their habitats, as well as the complex relationships among the organisms and between organisms and the natural environment. Under both natural effects and human influences, the stability and variability of the river ecosystem has been extensively concerned. So far, there have been some single or compound indicators, with certain pertinence and universality, used to characterize the eco-environment quality and biodiversity level of the river. But as the eco-environment of the river is constantly changing, especially caused by the human disturbance, several large species in the river have been “extinction”, or “most likely extinction”, or “critically endangered”, therefore, at this stage, it is necessary to establish a new ecological assessment indicator based mainly on the survival conditions of existing large species in the river. The new indicator will be used to comprehensively characterize the health status and biodiversity integrity of the river ecosystem, and to provide scientific and technological support for the well implementation of the “10-year fishing ban” and the “Yangtze River Protection Law”. The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) only distributes in the middle and lower reaches of the Yangtze River, Dongting and Poyang Lakes, and likely, has been the only aquatic mammal in the river. Over the years, the porpoise has received high attention from all walks of life and has become a “star” species in the river. The changes of porpoise population distribution and size are closely related to the changes of eco-environment and fish resources in the river, which have the basic attributes of comprehensively representing the eco-environmental quality, fish resources, biodiversity and their changes. In the complex underwater acoustic environment, the sonar signals of the porpoise have distinct time-frequency characteristics and are easily detectable and quantifiable. The sonar signals have been widely used for passive acoustic monitoring and real-time identification, as well as group size estimation of the porpoise in the wild. Meanwhile, the employment of the passive acoustic monitoring for detection of the porpoises in the wild is convenient and highly efficient, and even for non-professionals with short term training. Long-term employment of underwater passive acoustic monitoring in sample sites along the river and in the lakes can detect the occurrence of the porpoise, group size and their changes. The detection results can be used not only for quantitative analysis of eco-environmental quality, fish resources and aquatic biodiversity in the sample sites, but also for quantitative evaluation of the anthropogenic disturbance to the eco-environment and aquatic biodiversity. Therefore, the population distribution and size of the porpoise based on passive acoustic monitoring can be employed as an important ecological assessment indicator to evaluate the eco-environmental quality and aquatic biodiversity, as well as their temporal-spatial changes along the river and in the lakes. Meanwhile, the indicator could be used to evaluate the implementation of relevant protection work and the actual protection effect.