Changes in stocks and sources of soil organic carbon (OC) with sea level rise (SLR) are crucial to carbon processes and sequestration benefits in mangrove forests. Soil OC contents and stocks were compared among three 11 years-old Kandelia obovata mangrove forests with SLR of 0, 40 and 80 cm, respectively, simulating the current, future ~100 years’ and future ~200 years’ SLR of mangrove forests along Jiulong River Estuary, an important K. obovata area in Fujian, China. Contribution rates of mangrove plants and allochthonous suspended particulate organic matter in tidal water (SPOM) to soil OC were also estimated. Significantly higher soil OC contents and stocks were measured at site SLR 80 cm. Mean OC stocks at sites SLR 80 cm, SLR 40 cm and SLR 0 cm were 23.82, 16.68 and 17.85 kg C m−2, respectively. High soil labile organic carbon (LOC) contents were also found at site SLR 80 cm, while low profiles of soil δ13C values were measured at site SLR 40 cm. Mean contribution rates of mangrove plants to soil OC were 36.65%, 35.42% and 21.79% at sites SLR 80 cm, SLR 40 cm and SLR 0 cm, respectively, and significantly higher OC contribution rates of mangrove plants were found at site SLR 80 cm. These indicated that SLR will increase soil OC stock and mangrove contribution to soil OC.