The identification of limiting factors is essential for the ecological restoration of riparian ecosystems degraded by the damming of rivers, but remains unclear. Here, we quantitatively assessed the relative importance of environmental factors and revealed the main limiting factors for riparian vegetation restoration and their influencing mechanisms, using riparian plant and environmental data of seven large reservoirs in southwest China. We found that inundation duration had a significantly greater effect on riparian vegetation distribution, cover and diversity than environmental factors such as inundation depth, rainfall, humidity, temperature, sunshine hours, aspect, slope, surface relief, soil pH, available nitrogen (AN), available phosphorus (AP), and available potassium (AK); vegetation cover, species richness, complexity and dominance were highly significantly negatively correlated with inundation duration (p < 0.01); inundation for 5 months is close to the tolerance limit of most plants and poses a significant limiting effect on the vegetation restoration in the reservoir riparian. Therefore, the inundation duration should be highlighted in riparian vegetation restoration. Meanwhile, incorporating the riparian inundation into the river ecological scheduling objectives to shorten the inundation duration and thus radically alleviate the limitation is a new opportunity for vegetation restoration in the reservoir riparian.