•Roots of P. australis enhance Fe-OC coupling, especially in low-tide areas.•Rhizosphere Fe-OC fluctuates seasonally, higher in low-tide flats in the growing season.•Plant growth stages significantly influence Fe-OC dynamics in tidal flat wetlands.•Significant rise in FeRB abundance in low-tide flat during non-growing season.•Seasonal shifts in microbial communities affect Fe-OC content in tidal sediments. As sea levels rise, coastal tidal wetlands are increasingly threatened by flooding and salt stress, highlighting the importance of iron (Fe) (hydr-) oxides in soil for stabilizing organic carbon (OC). This study focuses on Phragmites australis, common in the Yangtze River Estuary, exploring the interplay between OC and Fe (hydr-) oxides in the rhizosphere of P. australis across various seasons and elevations. It also examines microbial community shifts in the Fe oxidation–reduction cycle. Results show that in the non-growing season (January), Fe (hydr-) oxides and total organic carbon (TOC) levels in the rhizosphere soil of high-tide P. australis are significantly higher than during the growing season (August), with a notable increase in Fe oxide-bound OC (Fe-OC). The content of Fe-OC in tidal wetland soil fluctuates with plant growth stages and elevation. Notably, during the growing season, the Fe-OC content in the rhizosphere of low-tide P. australis is markedly higher than in high-tide areas, reversing in the non-growing season. The presence of P. australis roots is found to significantly enhance the accumulation and coupling of Fe (hydr-) oxides and OC, especially in low-tide areas compared to bare flats. This coupling is affected by the organic matter contributed by roots, microbial metabolism, and redox conditions of the soil. The study also highlights how plant and microbial metabolism regulate the response of rhizosphere Fe-OC across different tidal flat elevations. In low-tide environments during the non-growing season, the prevalence of Fe-reducing bacteria results in decreased Fe-OC content, while in high-tide areas, increased organic matter input boosts complexed Fe-OC formation. Overall, this study emphasizes the significance of plant metabolism in understanding the impact of sea level rise on Fe-OC stores in tidal wetlands, a vital factor for comprehending C cycling mechanisms and assessing C sequestration potential under future climate change scenarios.