The importance of mangroves in blue carbon storage has been widely reported. However, the potential contribution of microbial extracellular polymeric substances (EPS) to the carbon pool is still poorly understood in mangrove ecosystems. Thus, a natural mangrove reserve located in Gaoqiao was chosen to investigate the linkage between microbial EPS and sediment organic carbon. Sequential resin extraction, Fourier transform infrared spectroscopy (FTIR), and 16S high-throughput sequencing were employed to determine the variations in EPS and bacterial taxa in different mangrove communities. Both EPS and EPS-C increased significantly with mangrove zonation from seaward to landward, irrespective of the EPS subfractions (colloidal and bound EPS) and components (extracellular protein and polysaccharide). Moreover, both EPS and EPS-C were found to be positively correlated with soil organic carbon. The present data further showed that EPS-C accounted for 1.84~10.69% of TOC in surface sediments. Multiple functional groups (e.g., O-H, N-H, and C=O), which may provide ligands for particle adsorption and complexation, were identified by FTIR. Consistent with the ascend of EPS with mangrove zonation from seaward to landward, the highest transmittance intensity for all functional groups was consistently exhibited in EPS isolated from landward Rhizophoraceae forest. In addition, the present data also indicated an interesting positive linkage between EPS and the abundance of some specific bacterial taxa, such as Rhizobiales, Corynebacteriales, and Gaiellales. In summary, this study claims the importance of EPS in the carbon pool in mangrove ecosystems. The present study may provide a better understanding of the functions of mangroves in carbon stocks.