The water-level fluctuation zones (WLFZ) in Three Gorges Reservoir encounter several ecological challenges, particularly potential greenhouse gas (GHG) emissions and water eutrophication due to water level variations. Therefore, to address those challenges, our study explores the relationships between soil properties (Phosphorus cycle), plant conditions, microbial community, and GHG emissions. Our findings reveal that aboveground plants are the key link in the WLFZ ecosystem, which has previously been overlooked. Hydrological variations are continuously resetting the soil microbial system, keeping their ecological function in a primary state. Variations in elevation and soil nutrients have a minimal impact on GHG emissions in harvested plant areas. In contrast, in native plant areas, these variations significantly influence both GHG emissions and the phosphorus cycle. A strategic harvesting approach targeting high and low-elevation areas is also proposed, focusing on plants with high phosphorus enrichment coefficients (EC