Abstract: The threat posed by sea level rise (SLR) under climate change to the mangroves in tropical and subtropical intertidal zones and their carbon sequestration capacity is becoming increasingly significant. To understand the impact of SLR on mangroves and their carbon stock distribution, this study focuses on the Zhanjiang Mangrove National Nature Reserve in Guangdong Province, China, where it has the largest protected area of mangroves in China. Using data from field surveys, remote sensing observations, and climate models, this study assessed the effects of SLR under different greenhouse gas emission scenarios (SSP1-2.6, SSP2-4.5, and SSP5-8.5) on mangrove area and the spatial patterns of total carbon storage. Results indicate that: ① Under different climate scenarios, SLR will lead to significant losses of mangrove areas in Zhanjiang by the end of this century, with estimated reduction ranging from 10.48% to 28.94%. Notably, SSP1-2.6 and SSP2-4.5 scenarios show substantial area losses in the southern Leizhou Peninsula, Xuwen, and Mazhang districts. Under SSP5-8.5 scenario, extensive area losses will occur across all areas except for Zhanjiang Port. ② Under different climate scenarios, mangroves in Zhanjiang are expected to remain a net carbon sink. However, relative losses in carbon stocks will be substantial by the end of the century, with projected reduction ranging from 29.96% to 72.09% compared to current levels. The losses concentrate in the southern Leizhou Peninsula, Xuwen, and Mazhang districts under SSP1-2.6 and SSP2-4.5 scenarios, while under SSP5-8.5 scenario, significant losses occur across all areas except for Zhanjiang Port. ③ The spatial patterns of mangroves carbon stocks will be significantly changed by SLR, with a decrease in the concentration of similar carbon stock values. Low-value concentration areas will increase, while high-value concentration areas will shift toward the land. The analysis suggests that differentiated dynamic adaptive management strategies should be considered for the protection and nurturing of mangroves to mitigate the future impacts of SLR.