This study used microcosm experiments and field flux measurements in Chongming salt marsh in the Yangtze Estuary to assess how flooding and increased salinity impact carbon processes. Results indicate that photosynthesis in Phragmites reeds was more sensitive to water-salt stress than respiration, with significant reductions in photosynthetic rates, leaf area, and overall productivity, especially under combined flooding and high salinity conditions. Soil respiration was similarly suppressed by flooding and salinity, although periodic re-aeration after flooding caused brief emission spikes. Overall, increased flooding and salinity more strongly reduced carbon sequestration than carbon emissions, lowering net ecosystem carbon exchange and limiting carbon allocation to soils. Under future sea-level rise scenarios, the combined stress from flooding and salinity could significantly weaken the carbon sink function of coastal salt marsh ecosystems.