As an important component of global change, plant invasion threaten the sustainability of global ecosystems and may alter the carbon dynamics in the invaded area. Knowledge of the effects of Spartina alterniflora invasion on soil organic carbon (SOC) and soil inorganic carbon (SIC) stocks and their profile distribution is limited in coastal salt marshes, which are referred as important “blue carbon” ecosystems. A short-term invasion chronosequence of 2–10 years was used to evaluate the responses of SOC and SIC over the invasion period in the Yellow River Estuary, China. The ¹³C isotope content was analyzed in soil, plant tissue, and sediment debris to infer the contribution of invasion to SOC accumulation in the invaded salt marshes. The results showed that more than 80% of the soil C was inorganic, and this percentage was higher in native sites and in the newly invaded areas. SOC accumulated linearly with the invasive time in the top 100 cm soil. The SOC accumulation rate varied along the soil profile, and was 0.10, 0.13, and 0.40 kg C m⁻² yr⁻¹ in the top 20cm, 40cm, 100cm soils, respectively. The ¹³C isotope analysis demonstrated that debris-derived C was dominant in the native salt marshes (62.2% on average), while plant-derived C increased with the invasive time. Structural equation modeling (SEM) showed that the SIC loss in the top 40 cm with invasion could be indirectly attributed to the soil acidification in the alkaline soil and directly related to soil Ca loss. Our results also suggested that SIC loss would partially offset the CO₂ sequestration associated with SOC burial caused by the invasion. This work indicates causal relationships between plant invasions and soil carbon pools and highlights the nonnegligible importance of inorganic C in coastal blue carbon budgets.