Abstract: Coastal wetlands play a crucial role in mitigating climate change due to their “blue carbon” function. However, the carbon sequestration capacity of these ecosystems is threatened by the invasion of Spartina alterniflora. Salt marshes represent the largest type of coastal wetland in China. To comprehensively assess the impact of Spartina alterniflora invasion on the carbon sequestration capacity of salt marsh ecosystems, we conducted measurements and analyses of carbon flux (e.g., methane CH₄ and carbon dioxide CO₂), vegetation biomass, and soil organic carbon (SOC) content in typical salt marshes (including marshes invaded by exotic Spartina alterniflora for 10 a and 20 a, as well as native mudflat, Suaeda salsa marsh and Phragmites australis marsh) in Yancheng and assessed the carbon sequestration potential at the regional scale. The study results revealed that the total carbon emissions (comprising CO₂ and CH₄ fluxes) from Spartina alterniflora salt marshes (1.16-2.58 kg/(m²·a)) were lower than those from Phragmites australis salt marshes (10.60 kg/(m²·a)) but higher than those from bare mudflats and Suaeda salsa salt marshes (0.75 and −0.60 kg/(m²·a), respectively). Compared to the native salt marshes, the invasion of Spartina alterniflora led to an increase in the storage of both vegetation and soil carbon pools. Specifically, the high primary productivity of Spartina alterniflora significantly enhanced biomass carbon accumulation above and below ground. Concurrently, SOC content in the invaded marshes showed a notable increase compared to the native mudflat and Suaeda salsa marsh, particularly in the upper soil layers, although the magnitude of this increase varied with the duration of invasion. From an ecosystem carbon budget perspective, the annual carbon emissions from Yancheng coastal salt marshes (0.44 Tg/a) were lower than the total annual carbon input (0.76 Tg/a), attributed to carbon fixation associated with the expansion of Spartina alterniflora and the negative emissions from Suaeda salsa salt marshes. Despite the current net sink status, a historical analysis of carbon stocks revealed a significant decline in the overall carbon sequestration potential of the Yancheng coastal salt marshes. By 2021, the total estimated carbon sequestration potential was 3.73 Tg. This represents a substantial reduction of 51.6% compared to the estimated potential in 1987. This dramatic decrease is primarily driven by large-scale losses in the areal extent of native salt marshes due to land reclamation, coastal development, and ecological degradation. Crucially, the increase in carbon sequestration resulting from the areal expansion of Spartina alterniflora (contributing an estimated +1.39 Tg) was insufficient to offset the massive carbon sink loss caused by the shrinkage of native Suaeda salsa and Phragmites australis salt marshes (estimated at -1.59 Tg collectively). In addition to the direct loss of soil carbon stocks resulting from wetland area shrinkage due to anthropogenic reclamation, the long-term environmental changes in wetlands under Spartina alterniflora invasion also indirectly weakened the regional carbon sequestration function. The findings provide crucial scientific evidence and foundational data support for the management of carbon sequestration resources and the conservation of coastal salt marsh ecosystems.