In order to clarify the long-term changes in mangroves in the Beibu Gulf of Guangxi and the carbon storage changes after the invasion of Spartina alterniflora (S. alterniflora) in the Dandou Sea area, the Continuous Change Detection and Classification (CCDC) algorithm combined with feature indices was first used to track the changes. Subsequently, the random forest algorithm was applied to classify each change segment, and then sampling was conducted based on the distribution of S. alterniflora in different invasion years. The results showed that the Kappa coefficient of the classification result of the latest change segment was 0.78. The rapid expansion of S. alterniflora, aquaculture pond construction, and land reclamation activities have led to changes in mangroves, causing a decrease in the area of the mangrove region. A total of 814.57 hectares of mangroves has been converted into other land-cover types, with most pixels undergoing one to two changes, and many of these changes were expected to continue until 2022. An analysis of the distribution characteristics and influencing factors of soil organic carbon (SOC) and soil organic carbon storage (SOCS) at different invasion stages revealed that SOC and SOCS were mainly influenced by soil bulk density, soil moisture content, and electrical conductivity. It was found that S. alterniflora had higher SOC content compared to the mudflats. With the increase in invasion years, S. alterniflora continuously increased the SOC and SOCS content in coastal wetlands.