Sea-level rise (SLR) may offset gains made by enhancing mangrove carbon sequestration through greater greenhouse gas emissions. However, accurate prediction of greenhouse gas (GHG) fluxes under future SLR is still relatively uncertain. In this study, we implemented a series of “marsh-organ” designs (experimental platforms at different elevations) along a latitudinal gradient in China, simulating four sea-level scenarios. We investigated the factors driving the patterns observed in ecosystem respiration (R_eco), methane (CH₄), and nitrous oxide (N₂O) fluxes from mangroves and adjacent mudflats. We examined environmental factors, soil properties, and net ecosystem productivity (NEP), and we used structural equation models to map functional process impacts on GHG fluxes. Our findings revealed that SLR reduced NEP, R_eco, and N₂O fluxes while increasing CH₄ emissions in both mudflat and mangroves. SLR and latitudinal distribution significantly altered biological and abiotic factors that influenced GHG fluxes. The present R_eco for mudflat and mangroves ranged from 230 to 1640 g m^-2 year^-1, with 0.32 to 0.88 g m^-2 year^-1 in CH₄ emissions and 0.02 to 0.29 g m^-2 year^-1 in N₂O emissions. The net global warming potential (GWP) from current mangrove GHG emissions is -10,897 to -1093 gCO₂ m^-2 year^-1 at Yunxiao, followed by -4113 to -246 gCO₂ m^-2 year^-1 at Haikou and -987 to -83 gCO₂ m^-2 year^-1 at Aojiang. SLR stimulated CH₄ emissions in mangroves increased by 20% in RCP 4.5 and by 12% in RCP 8.5, versus the current sea level by 2100. In contrast, SLR markedly inhibited R_eco and N₂O emissions by 42% to 56% and 23% to 32%, respectively. Moreover, NEP experienced a decrease from 27% to 50%, indicating a projected 24% to 51% reduction in the capacity for mangroves to mitigate climate change through reduced GHG emissions with SLR in the future.