The construction of the Three Gorges Dams in the Yangtze River in the 1990s has induced profound impacts on the environment and biodiversity in the reservoir region, although these hydroelectric dams have supplied an enormous amount of hydropower resources and electricity to all of China. One main example of such environmental effects is the gradual degeneration or death of plants under waterlogging or flooding along the reservoir areas after implementation of the dams. The river banks, which serve as hydro-fluctuation belts, have been annually fluctuated for three to six months at a time, leading to low soil fertility and high erodibility. Meanwhile, some adaptive vegetation with low water-holding capacity has persisted in the drought soil. However, these distinctive characteristics are major restoration obstacles in the hydro-fluctuation belt area, even for plants with strong vitality. Mulberry (Morus alba L.), a plant native to China, has not only economic importance to the Chinese silk industry but also ecological benefits to its plantation regions in China. Studies have shown that mulberry trees have strong ecological adaptation ability and ecological restoration potential, as they are able to hold water and prevent soil erosion with their extensive root systems. These traits facilitate mulberry survival in harsh environments, particularly when they have established symbiotic associations with beneficial soil microorganisms such as arbuscular mycorrhizal (AM) fungi. On the other hand, the application of AM fungi to ecological restoration has been recently proposed. In general, AM fungi and their massive underground hyphal networks could enhance the uptake of plant nutrients and water, formation of soil aggregates, and resistance to biotic and abiotic stresses. Studies have further shown that AM fungi have significant impacts on the soil microflora community and on plant community compositions. As a result, mulberry trees colonized by AM fungi could have the capacity to improve the soil rhizosphere quality, promote the uptake and transportation of minerals and water, and enhance the tolerance to drought and waterlogging. Therefore, mycorrhizal mulberry could promote leaf development and tree performance for the food resource of silk worms as well as function in ecological restoration on the river bank areas of the Three Gorges Reservoir. As the growth rate of mulberry is inversely related to fluctuations of water level in the reservoir, the planting of AM fungi-colonized mulberry trees is considered to be a potential ecological restoration strategy to deal with both the waterlogging in winter or early spring and the drought in summer at the fluctuation belts or in other fragile ecosystems of the Three Gorges Reservoir. In this paper, we review the ecological characteristics and plant growth obstacles faced during the water fluctuation period on the river banks along the Three Gorges Reservoir areas of the Yangtze River, and then propose the potential application of the mycorrhizal mulberry for ecological reconstruction of the hydro-fluctuation belts of these areas.