Coastal wetlands, recognized as globally significant carbon sinks, have experienced substantial alterations in ecosystem structure and function due to Spartina alterniflora invasion. This study investigates the impacts of S. alterniflora invasion on soil organic carbon (SOC) after 4, 9, and 14 years. Post-invasion, SOC content in the 0-20 cm soil layer increased by factors of 1.71, 4.03, and 6.24 compared to mudflat, and by 1.39, 3.26, and 5.05 compared to native Suaeda salsa. Labile SOC fractions exhibited significant correlations with SOC, and while the invasion did not modify the types of SOC functional groups, it altered their relative abundances. In the 0-40 cm soil layer, SOC stocks under S. alterniflora after 4, 9, and 14 years of invasion reached 1.30, 1.50, and 1.83 kg center dot m- 2, respectively, surpassing those of native mudflat (0.91 kg center dot m- 2) and S. salsa (1.09 kg center dot m- 2). The invasion of S. alterniflora demonstrates short-term benefits but long-term shifts in SOC stability. During the initial invasion phase, the top-layer (0-40 cm) SOC exhibited enhanced stability. However, as the invasion advanced, the sub-layer (40-100 cm) SOC stability declined, revealing disadvantages relative to native S. salsa and mudflat. Furthermore, the invasion markedly modified soil physicochemical properties, with salinity emerging as a critical factor influencing SOC and its stability. The study reveals that S. alterniflora invasion enhances carbon sequestration, predominantly in the 0-20 cm. Short-term invasion moderately improves SOC stability without significantly affecting SOC accumulation, whereas long-term invasion diminishes SOC stability. Consequently, over the long term, S. alterniflora invasion undermines the development of a stable SOC pool.