Abstract: Carrying out tracking station research on water ecological environment in cities along the Yangtze River is a concrete manifestation of implementing the spirit of President Xi Jinping′s important instructions on "Great Protection of the Yangtze River". The whole area of Jiujiang City, a city in the middle reaches of the Yangtze River was taken as the research area. On the basis of data collection and field research, and applying information technology, statistical analysis, numerical simulation and other research methods, a systematic research was conducted mainly on database construction, station research platform construction, water ecological environment problem diagnosis, pollutant traceability analysis, and comprehensive scheme formulation. The research ideas of the mutual nesting of the demands of the stagnation city and the joint research tasks of the Yangtze River ecological environment protection were explored. The technical route and the method system of "data platform construction → global problem diagnosis → layer-by-layer two-way analysis → comprehensive policy implementation in the whole-process" for "pulse examination, inquiry, and prescription" for urban water environment problems was established. A set of comprehensive solutions of "one city, one policy" that coordinated the three dimensions of "structural emission reduction, technical emission reduction, and management emission reduction" and followed the whole-process governance of "source prevention, process control, and end management" were proposed. The research could provide reference for the same type of research in cities with complex water ecological environment.