The water-level fluctuation zones in the Three Gorges Reservoir are facing a number of ecological problems following establishment. Ecological restoration practice is the key to solve these problems. Theoretically, species selection is critical for ecological restoration. However, the results of plant adaptation capability to the water-level fluctuation zone by yearly community observations in the past few years did not match those obtained from flooding simulation experiments, nor are they consistent with the short-term in situ planting experiments. One of the reasons leading to such inconsistency is that the practical water-level scheduling is different from the scheme adopted in the flooding simulation experiments with regards to the flooding rhythm, duration and depth. An analysis on the practical water level over four years in Zong Xian of Chongqing revealed that: a) there existed a large difference between the practical and theoretical water-level scheduling; b) the submerged days at the elevation of 146, 152, 158, 164, 170 and 176 m during the non-growing season (from October to the following April) were 294, 266, 223, 167, 101 and 0, respectively. The flooding days at those sites during the growing season flooding were 68, 20, 11, 1, 0, and 0, respectively. Sites below the elevation of 164 m suffer frequent waterlogging during the growing season. Currently, most flooding simulation experiments only emphasized the short-term shallow submergence during growing season, neglecting deep submergence during non-growing season. In fact, many studies have proven that significant differences in the responses of plants to submergence existed between the growing and non-growing seasons, as well as between deep and shallow submergence. Further, flooding simulation experiments did not account for in situ inter-specific relationship and community assembly. Accordingly, the flooding simulation experiment for species selection strategy has some shortcomings. Based on the analysis, we suggest that the species selection strategy design in the future should emphasize on: 1) the mechanisms attributing to adaptation of species to the water fluctuation zone during non-growing season; 2) the growth recovery, expansion and colonization of species following release from submergence; and 3) long-term observations on plant community and field grown plants. Long-term observations of field grown plants need to be taken seriously. Studies of species distribution, population and community dynamics, as well as landscape pattern, using plant functional type method, have an important role in guiding the ecological restoration practice in the water fluctuation zone, and are an important part of ecological research in the Three Gorges Reservoir area.