Mangrove swamps and salt marshes are noted for their large carbon sequestration and storage capacity. In southeastern China, mangrove transplantation is conducted as ecological restoration where exotic Spartina alterniflora (hereafter Spartina) is removed. This study aimed to evaluate the effectiveness of mangrove transplantation on carbon sink potential. We analyzed chronological sediment accretion, soil carbon sequestration, and carbon storage of mangroves and Spartina on Maoyan and Ximen islands. Results showed that on both islands mangroves and invasive Spartina stored 12.7%–31.4% more carbon than bare mudflats over top meter soils, with Spartina outperforming restored mangroves. Both restored mangroves and invasive Spartina enhanced sediment accretion, but this enhancement was minimal in high sediment supply areas like Maoyan. Spartina invasion improved carbon sequestration capacity compared to bare mudflats in Maoyan, but mangrove restoration failed. In low sediment supply areas like Ximen, restored mangroves have outperformed Spartina invasion on carbon sequestration enhancement since >5 years of planting. Thus, carbon sink potential of mangrove restoration depended on sediment supply and time, with sediment supply being more important. We suggested that it was preferable to conduct mangrove restoration with Spartina eradication in low sediment supply areas in subtropics.