After the completion of the Three Gorges Dam, a hydro-fluctuation belt with a range of 30 m and an area of about 350 km² was formed. The unique anthropogenic hydrological regime of the Three Gorges Dam has had significant negative impacts on the reservoir's ecosystem. A large number of native flooding-intolerant plants living within the belt have gradually died due to off-season flooding, which negatively affected the ecosystem structure and function of the hydro-fluctuation belt. Therefore, vegetation reconstruction and restoration in the Three Gorges Reservoir (TGR) is urgent; previous studies have shown that Salix matsudana has been used for vegetation reconstruction due to its flood resistance abilities. The nutritional accumulation and distribution of plants in a certain degree can reflect eco-physiological processes, and can serve as a crucial indicator of the structure and function of the local ecosystem. In order to explore how S. matsudana adapts to the winter flooding in the hydro-fluctuation belt of the TGR through the accumulation and distribution of nutrients, the growth status and the nutrient content in leaves, branches, and roots of S. matsudana in three sampling belts (at altitudes of 175 m, 170 m, and 165 m) of the vegetation remediation demonstration base of the TGR were measured in May 2015. The results showed that:(1) After three flooding cycles, the plant height, base diameter, and crown width of S. matsudana were inhibited by the increase of flooding intensity; however, compared with the initial stage of planting, the plant height, base diameter and crown width of S. matsudana in the three sampling belts were significantly higher, and the growth status was good as well. (2) The nutrient content in all organs of S. matsudana were maintained at normal levels, but flooding reduced the content of N and P in roots and increased the Fe and Mn content. In addition, winter flooding resulted in a significant decrease in the content of Ca in S. matsudana leaves and branches and the content of Cu and Zn in the branches and roots at an altitude of 165 m. (3) Under flooding stress, N, P, K, and Mg elements accumulated more in the leaves, while Cu and Zn accumulated in the branches, which is beneficial for photosynthetic rates and recovering growth of plants after water withdrawal. While winter flooding leads to higher accumulation of Fe and Mn elements in the roots, this disturbance to normal root physiology deserves further attention. Studies have shown that under different flood stress conditions, S. matsudana can adjust the accumulation and distribution of nutrients in a targeted manner to ensure a normal growth state. However, in this study of vegetation restoration and reconstruction in the water-fluctuating zone of the reservoir, we found that it is necessary to strengthen the monitoring and research of sustainable growth of S. matsudana at altitudes below 170 m.