Extreme rainstorms can flush intertidal sediments and drive the transport of large amounts of organic matter from land to sea. Mangrove wetlands, one of the most important “blue carbon” habitats, are located in the intertidal zone and serve as an ecological corridor connecting land and sea. In this study, we investigated the effects of extreme rainstorms on organic carbon compositions, source-sink processes based on the MixSIAR model, and the production of greenhouse gases, including carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), using mangrove sediments. The results showed that in the intertidal zone, the total contents of sediment organic carbon, mineral-bound, and fine-particle organic carbon, humic acid, and humin were improved by the influence of an extreme rainstorm. The contents of coarse sediment organic carbon (SOCcoarse) and fulvic acid were decreased and were exported from intertidal zone to the sea. In tidal creek zones, extreme rainstorms enhanced the mean production rates of CH4 and CO2 by 817.4% and 34.3%, respectively, owing to the increased terrestrial organic matter, including SOCcoarse and humic acid. The N2O production rate was decreased by 72.2% in the creek zone because of the loss of total nitrogen after an extreme rainstorm. These findings provide new insights into SOC components, mechanisms of greenhouse gas production, and their response to extreme rainstorms, which will be helpful for the management of coastal wetlands and our understanding of how frequent extreme weather controls wetland biogeochemical processes.