We investigated and quantified soil organic carbon (SOC) stock at the mangrove forest (Magyi, That Bot Khan and Wette) of Shwe Thaung Yan coastal region in Myanmar and estimated the SOC stock changes in Magyi mangrove forest over six years using repeated field measurements. The study sites were characterized by different mangrove vegetation, soil types, and sediment deposition from different water sources. Results showed that the mangrove preservation and restoration efforts had a significant effect on soil C storage, with soil carbon stocks in 2021 (1954.43 ± 33.24 ton/ha) being 2.7 times higher than the estimated carbon stock in 2015 (732.26 ± 6.99 ton/ha). The results also revealed slight differences in SOC between Magyi and the Tha-Bot-Khan and Wette areas, as the mangrove plants in the latter areas have an additional source of nutrients from Pho-Thoung-Gyi, a deep-sea bay near the forest. Our research findings are beneficial in understanding the role of Myanmar’s mangrove ecosystems in carbon sequestration and climate change mitigation efforts.