The water fluctuation zones are widely distributed in the Yangtze River Basin, with diverse types, different kinds of formation, various functions and complex habitats. The intensive analysis of the historical changes, current situation and component types of the water fluctuation zones is of great significance for maintaining the aquatic biodiversity and ecosystem balance along the banks of rivers and lakes, and protecting the ecological and environmental security of the Yangtze River system. In this paper, the medium-large scale remote sensing monitoring method is used to investigate and analyze the water area and the fluctuation area of the Yangtze River Basin, focusing on the change trend from the natural water body to the artificial water surface, and its potential impact on the decline of the natural fishery resources in the Yangtze River Basin. The results show that, in the past 40 years, the historical maximum water surface of the whole Yangtze River Basin is about 63,360 km², the minimum water surface is about 26,396 km², and the historical maximum ebb and flow area is about 36,964 km². From 2019 to 2020, the "One River, Two Lakes and Seven Rivers" region had a maximum water surface of 19,663 km², a minimum water surface of 14,281 km², and a fluctuation area of 6,337 km², including an anti-seasonal fluctuation area of 633 km². Compared to period of 2001-2020 and period 1984-2000, more than 80% of the reduction of surface water was due to the loss of the area of seasonal natural water fluctuation, while the increase that resulted from reservoir filling was up to 5500 km². As a result, the structure of water ecosystem in the Yangtze River basin changed dramatically. The proportion of natural water body and fish resources was less than half of that in the 1980s. Furthermore, this study clarified the concept of anti-seasonal artificial water fluctuation area for the first time, and investigated the relationship between the anti-seasonal artificial water fluctuation zone formed by the filling of cascade reservoirs in the Yangtze River Basin and the loss of fish critical habitat.