Phylogenetic structure incorporating phylogenetic data in the studies of community provides a new perspective for biodiversity research. To explore the maintenance mechanisms of species diversity of riparian plant communities under the flooding disturbance, the original riparian vegetation in Danjiangkou Reservoir before the first phase of the Middle Route of the South-to-North Water Diversion Project was investigated. The phylogenetic structure and species diversity of riparian communities and their relationship with environmental factors under the flooding disturbance were analyzed. The results indicated that:(1) with the increase of the intensity of flooding disturbance, the species richness, species diversity, and phylogenetic diversity of the riparian communities decreased significantly. Although there was no significant difference in the net relatedness index of communities, the phylogenetic structure communities showed a trend from divergence to aggregation with the increase of flooding disturbance intensity. The results indicated that the maintenance mechanism of species diversity in the riparian plant community was driven by habitat filtration and niche differentiation. And the ecological process effect of habitat filtering increased and the competition between species weakened with the increase of flooding disturbance intensity. (2) The species richness, species diversity, and phylogenetic diversity of all plant communities in the riparian zone were significantly affected by slope, soil texture, available nitrogen content, and total nitrogen content. In addition, the species richness was significantly affected by soil thickness and available phosphorus content, and the phylogenetic diversity was significantly affected by soil thickness. However, only available nitrogen content had a significant effect on the net relatedness index. Slope aspect, available phosphorus content, and the three diversity indices were significantly correlated under the light flooding disturbance. Slope, soil thickness, soil texture, total nitrogen content, and three diversity indices were significantly correlated, and soil pH, total nitrogen content, available phosphorus content, and net relatedness index were significantly correlated under the moderate flooding disturbance. Soil texture, available nitrogen content, total nitrogen content, and the three diversity indices were significantly correlated. The environmental heterogeneity under different flooding disturbance intensities resulted in different mechanisms of community construction and diversity maintenance in riparian zones. The study provides the theoretical reference and a scientific basis for biodiversity conservation in the riparian zone of the reservoirs.