The water-level fluctuation zone of the Three Gorges Reservoir is a unique ecosystem characterized by periodic flooding and drought stress, where topography strongly influences plant community dynamics. However, the connection between microtopography and plant diversity under varying hydrological regimes has received limited attention. Therefore, it is crucial to explore the connection between microtopography and both plant species diversity and functional diversity under different flooding intensities in the water-level fluctuation zone. This study investigates the effects of microtopography on plant species and functional diversity across different flooding intensities in the Wuyangba, located on the north bank of Hanfeng Lake in in Kaizhou District, Chongqing, which is affected by the changing water level of the Three Gorges Reservoir. We analyzed community composition, diversity distribution patterns along elevation gradients, and the relative contributions of topographic factors to diversity indices. The results indicated that: (1) plant community types significantly differ across microtopographic features; (2) significant differences were observed in species diversity index among different microtopographies, with the diversity index in concave and convex terrains being significantly higher than that in rugged slopes and flat terrains; (3) at elevation I, three species diversity indices and two functional diversity indices were significantly negatively correlated with topographic standard deviation (TSD); conversely, at elevations III and IV, the three species diversity indices and all functional diversity indices were significantly positively correlated with TSD; (4) elevation, TSD, and microtopography are the primary drivers of diversity, with the "elevation + TSD" combination having the strongest synergistic effect (R2 = 0.83, P < 0.001). These findings suggest that environmental heterogeneity enhances community stability and resilience in the zone. This study provides critical insights into the spatial distribution patterns of plant communities and their diversity across microtopographies, offering a scientific foundation for ecological restoration and biodiversity conservation in the water-level fluctuation zone.