Spartina alterniflora has rapidly expanded in coastal wetlands of China, and this would affect soil organic carbon (SOC) storage and stability. In the present work, the impacts of S. alterniflora colonization on SOC pool and stability was deciphered to better understand how alien species altered the carbon cycle in the Yellow River Delta (YRD). SOC contents were in the range of 1.29g/kg-7.02g/kg, of which wetlands covered by S. alterniflora increased with colonization time and exceed those in wetlands covered by native species after 7years. Pyrolysis-gas chromatography/mass spectrometry analysis showed that aromatic moieties were predominant components of SOC, and there were remarkable increase trends of phenol and lignin compounds and decrease trend of aromatic moieties with S. alterniflora invasion time. SA had the highest microorganism biomass reflected by phospholipids fatty acid (PLFA) across different wetlands. Salinity had the largest negative effects while nutrients had the largest positive effects on the SOC pool. The proportion of decomposition-resistant compounds (including aromatics, lignin, and phenol) to total SOC was decreasing while the SOC pool was increasing with S. alterniflora invasion time. This study demonstrated that S. alterniflora invasion could promote the SOC pool but weaken its stability in the wetlands of the YRD.