The water level fluctuation zone of the Three Gorges Reservoir Area is a special geographical unit formed by water level fluctuations, which causes a special change rhythm of vegetation in the water level fluctuation zone in the reservoir area. However, there are few reports on the change characteristics of vegetation in the water level fluctuation zone of the Three Gorges Reservoir Area on small-medium scales in a long-term observation. In this study, we conducted an in-depth analysis of the vegetation changes in the water level fluctuation zone of the Three Gorges Reservoir Area by collecting and collating data from all relevant literature published between 2002 and 2022. The results revealed that significant changes occurred in the species composition, abundance, and coverage of riparian vegetation before and after impoundment, showing a marked decline. More vegetation species were recorded before impoundment, with a maximum of 481 species in the initial stage of impoundment. This was decreased to 77 species in 2022, representing a reduction of 81%. Meanwhile, the numbers of tree, shrub, and herb species declined by 86.8%, 90.7%, and 38.2%. Tree and shrub coverage showed a significant decrease, and herbaceous plant coverage significantly increased. The dominant vegetation has shifted from a co-led of woody and herbaceous plants to a community predominantly dominated by perennial and annual herbaceous plants, with Cynodon dactylon (L.) Pers. being the most dominant species, whose importance value increased from 9.38 before impoundment to 17.28 after impoundment. Additionally, there was a significant gradient change in vegetation coverage at different elevations, with the upper layer > middle layer > lower layer. There was a significant gradient change in vegetation species, with the upper layer (11 species)> middle layer (9 species)> lower layer (7 species). In the structural equation model, the duration of submergence was the most significant factor affecting vegetation change (the total effect of standardization is 0.46), which had an important impact on the change of species number and coverage. Therefore, the selection of adaptive species and the in-depth study of niche adaptability, vegetation characteristics, and environmental response is important in the ecological restoration of the water level fluctuating zone of the Three Gorges Reservoir Area. The results of this study provide information for understanding the alternation in vegetation community and restoration of the vegetation in the water level fluctuating zone.