To clarify influence of multi-year high water level running on growth recovery of dominant plants in water-level-fluctuating zone of the Three Gorges Reservoir, the quantitative changes of Cynodon dactylon population in Changshou area were investigated in 2008 and 2017. We also discussed the influences of high water level on the germination, growth, and material allocation of C. dactylon. The results showed that multi-year high water level running significantly promoted the formation and germination of adventitious buds which made more ramets to be formed. Multi-year high water level running significantly restrained plant height, stem width, and leaf number of the ramets, while leaf length and total leaf number of the population were significantly promoted. Furthermore, the leaf length was decreased with water level decreasing. However, the leaf width and total leaf number showed the opposite increasing trend. Simultaneously, multi-year high water level running led to the significant promotion of stem length, stem nodes number and total stem length of stolons and rhizomes. The stem length and stem nodes number of the stolons were decreased with the water level decreasing. On the contrary, stem length and stem nodes number of the rhizomes were increased with water level decreasing. As a result of high-water-level operation for many years, dry mass of the rhizomes showed an increasing trend, while dry mass of the ramets and the stolons showed an opposite decreasing trend. In addition, the proportion of the rhizomes, ramets in low water level, and stolons in high water level also showed an increasing trend in material distribution of the population. Therefore, C. dactylon not only have strong flood resistance and growth recovery ability, but also have strong colonization ability, which can be used as one of the primary native species for vegetation recovery and reconstruction of in low or middle water-level-fluctuating zone of the Three Gorges Reservoir.