Rising sea levels have increased the risk of intense flooding in tidal wetlands, potentially leading to rises in soil iron-bound organic carbon (Fe-OC) contents by inhibiting microbial activity. However, flooding-induced Fe-OC accumulation may be attenuated by root activities of tidal wetland plants, which remains under-investigated in tidal wetlands. Here we established manipulative “marsh organ” filed experiments with soils collected from an oligohaline tidal wetland and introduced the indigenous plant species Phragmites australis (Cav.) Trin. ex Steud. These “marsh organ” mesocosms were then subjected to three flooding water-level treatments over a period of 3.5 years. Overall, root biomass, root porosity, and rhizosphere ferric iron-to-ferrous iron [Fe(III):Fe(II)] ratio increased with flooding levels, indicating that enhanced flooding promotes root oxygen loss of tidal wetland plants. The abundances of Fe-oxidizing bacteria (Gallionella) and Fe-reducing bacteria (Geobacter) increased, whereas the abundance of sulfate-reducing bacteria (dsrA gene) decreased with increased flooding, indicating a diversion of Fe from Fe-sulfur associations towards microbially-mediated Fe redox cycling. The soil organic carbon (SOC) pool did not change with increased flooding; however, the Fe-OC-to-SOC ratio (fFe-OC) increased from 9 to 18%. The fFe-OC was strongly related to soil amorphous Fe(III) concentrations and the activities of soil C-acquiring enzymes, both of which were affected by rhizosphere Fe(III):Fe(II) ratios. Thus, increased root oxygen loss, along with enhanced flooding, facilitated increases in amorphous Fe(III) concentrations and C-acquiring enzyme activity. Increased soil amorphous Fe(III) concentrations further promoted Fe-OC accumulation, whereas increased soil C-acquiring enzyme activities reduced the labile organic C pool. Overall, the dominance of the Fe-OC pool increased under enhanced flooding, owing to increased oxygen loss from the roots. Therefore, we outlined that soil C stability will increase in tidal wetland ecosystems that are exposed to future sea-level rise.