This study compared the carbon sequestration capacity of mangrove forests and salt marshes in Xinfeng, Hsinchu County, and Gaomei Wetland, Taichung City, Taiwan. Through elemental analysis and particle size analysis, we investigated the differences in carbon sequestration between the two blue carbon systems, the variations with depth, and the discrepancies compared to relevant foreign studies. Our findings indicate that smaller sediment particles are more likely to store more organic carbon; the degree of tidal influence on a site affects the abundance of its organic matter sources. The proportion of labile organic carbon (LOC) in Taiwan's blue carbon systems is generally higher than that of refractory organic carbon (ROC), possibly due to the lack of stable organic matter supply from rivers in Taiwan's carbon sink system, as well as the influence of age and climatic conditions. The relatively low proportion of ROC in total organic carbon (TOC) suggests that these systems are not suitable for long-term organic carbon storage but may rapidly form a new carbon sink system within a few decades.