Aims <p>Soil carbon is the largest terrestrial carbon reservoir and a key regulator of climate. However, its low stability and severe organic matter deficiency in coastal saline-alkali soils greatly limit ecosystem functions. Although intercropping has been shown to improve soil quality and affect carbon cycling, how the forest-medicinal plant system, with its distinctive plant associations and ecological roles, regulates carbon pool stability in saline–alkali soils through specific biogeochemical processes remains unclear.</p> Methods <p>This study, based on field experiments, employs enzyme stoichiometry and amplicon sequencing techniques to investigate the pathways through which the forest–medicinal plant system influences soil properties, resource limitations, and carbon pool stabilization, with the aim of providing a practical model for the synergistic enhancement of carbon sequestration and ecological utilization in saline-alkali soils.</p> Results <p>The results showed that the composite system effectively improved soil salinity-alkalinity, moisture, and structural characteristics, and enhanced soil organic carbon, total carbon, total nitrogen (TN), ammonium nitrogen (NH₄⁺-N), and total potassium levels. Intercropping medicinal plants significantly altered the soil microbial community structure, increasing microbial richness and diversity, but also intensified microbial carbon and nitrogen limitations. Redundancy analysis revealed that TN, NH₄⁺-N, nitrate nitrogen, urease activity, vector length, vector angle, and fungal richness (Chao1 index) were important driving factors influencing the level of the soil carbon pool.</p> Conclusions <p>This study reveals that forest-medicinal plant intercropping regulates soil carbon stabilization through a dual-pathway mechanism involving both restructuring of soil nutrient patterns and microbial ecological regulation, thereby providing a reference for the development of carbon-sink-oriented eco-economic models in coastal saline–alkali lands.</p>