Although seagrass meadows are intense carbon sinks, information on the regional variability in seagrass blue carbon stocks and carbon sequestration remains limited. We estimated the organic carbon (Corg) stocks and carbon accumulation rates (CAR) of seven seagrass meadows along the subtropical coast of China's Zhanjiang City and analyzed the driving factors of variability in sediment Corg stocks in three seagrass meadows. Results showed that most Corg (99.83 %) was stored in the sediments, and the contribution of living biomass was minor. The average Corg stocks of living biomass and sediments across all sites were 0.04 ± 0.01 and 42.03 ± 25.07 Mg C ha−1, respectively, which were significantly lower than the world average (2.52 ± 0.48 and 194.2 Mg C ha−1). The sediment Corg stocks of the upper 1 m ranged from 24.26 to 157.12 Mg C ha−1 with substantial variability among sites: Liusha Bay (64.93 ± 22.31 Mg C ha−1) > Donghai Island (33.8 ± 10.65 Mg C ha−1) > Dongshen Ferry (27.35 ± 4.15 Mg C ha−1). The average sediment CAR was 53.47 g C m−2 yr−1, and the total CAR of 864.18 ha seagrass meadows was 260.76 ± 4.86 Mg C yr−1 in these studied sites. Physicochemical factors, such as high moisture content, salinity, CaCO3 content, and low dry bulk density, jointly inhibited the mineralization rate of Corg in sediments. Our study provides data from understudied regions to a growing dataset on seagrass carbon stocks and sequestration rates and highlights the significance of local and regional differences in seagrass blue carbon storage to accurately assess the climate change mitigation potential of seagrass ecosystems.