Flood events severely damage the biodiversity and ecological functions of wetlands, posing a major threat to the health and stability of wetland ecosystems. Plants play a crucial role in maintaining the stability and balance of these ecosystems by providing food and habitat for various organisms. Although the wetland plants’ responses to flooding events have been extensively studied, the multi-level ecological characteristics (on the community, population, and individual plant level) of these plants in response to flooding have not yet been investigated. In this study, the community structure and ecological characteristics of Bolboschoenus planiculmis under different flooding conditions and plant traits were studied. The results revealed significant differences in the community composition and species diversity under various flooding conditions. Under continuous flooding, the number of species was three times greater than under seasonal flooding conditions. Flood events showed a significant impact on population density and coverage of B. planiculmis. The population density and coverage were 76.10% and 66.70% higher in seasonal flooding conditions than in continuous flooding conditions. Under seasonal flooding conditions, the allocation of total biomass and bulb biomass was greater than that observed under continuous flooding conditions. The results of the correlation analysis and redundancy analysis (RDA) indicated that the water level is a critical factor influencing the variations in the multi-level ecological features of the B. planiculmis community under different flooding conditions. This study suggests that maintaining seasonal flooding is essential for the natural restoration of B. planiculmis wetlands. These findings demonstrate that flood events significantly affect the ecological characteristics of B. planiculmis and offer valuable guidelines for the near-natural restoration of Grus leucogeranus habitats.