Coastal wetlands possess significant carbon storage capabilities. However, in coastal soil-plant systems augmented with biochar and microorganisms, the mechanisms of these amendments and carbon participation remain unclear. This study utilized pot experiments to explore how Enteromorpha prolifera biochar and Arbuscular mycorrhizal fungi (AMF) affect soil organic carbon (SOC), carbon-related microbes, photosynthetic and osmotic system of Suaeda salsa. The results showed biochar reduced exchangeable sodium percentage by 6.9% through adsorption and ion exchange, and increased SOC content by 34.4%. The abundance of carbon-related microorganisms (Bacteroidota and Chloroflexi) was increased and carbon metabolizing enzyme (cellulase and sucrase) activity in the soil was enhanced. AMF significantly improved plant growth compared with CK, as evidenced by the enhanced dry weight by 2.34 times. A partial least squares pathway model (PLS-PM) and correlation analysis suggested that the combined effect of biochar and AMF could be outlined as two pathways: soil and plant. Biochar increased SOC, improved the growth of soil carbon metabolizing microorganisms, and further promoted the activity of carbon-related enzymes. Additionally, AMF facilitated nutrient absorption by plants through root symbiosis, with biochar further enhancing this process by acting as a nutrient adsorber. These combined effects of biochar and AMF at soil and plant level enhanced the photosynthetic process of Suaeda salsa. The transport of photosynthetic products to the roots can increase the carbon storage in the soil. This study provides quantitative evidence supporting the increase of carbon storage in coastal wetland soil-plant systems through a combined application of biochar and AMF.