Background As the climate crisis continues to escalate and extreme weather events become more frequent, the carbon cycle has emerged as a focal point in scientific research. As the largest carbon pool on Earth, the lithosphere is a key focus of cutting-edge scientific research on the “missing sink” in the global carbon cycle. Due to the strong habitat heterogeneity of karst ecosystems and the limitations of existing research methods, current studies on carbon cycling in karst regions lack systematic analysis of the differences in multi-interface carbon fluxes and their underlying mechanisms within karst systems, thus necessitating the urgent development of a systematic research framework to analyze the carbon cycle law in karst regions comprehensively.

Methods The study systematically searched major domestic and international literature databases using core keywords such as “karst carbon sink”“carbon transfer” and “carbonate rock weathering” combined with expanded terms including “rocky desertification grades”“vegetation restoration” and “hydro-biogeochemical coupling” to ensure coverage of multi-scale and multi-process research. During the screening process, priority was given to empirical studies published in the past decade. By analyzing domestic and international research trends and the characteristics of karst ecosystems, and integrating key technologies such as artificial rainfall simulations, isotope tracing and hydrochemical runoff methods, this study constructed a multi-factor coupled simulation system for karst carbon migration encompassing the “atmosphere-vegetation-soil-rock-water” interfaces, enabling dynamic tracking of carbon pathways under controlled environmental variables.

Results By integrating key factors such as bedrock exposure rate, vegetation coverage, rock-soil contact area, and soil thickness, karst systems with varying degrees of rocky desertification were established. Techniques such as carbon isotope δ¹³C tracing have been systematically employed to monitor the migration patterns and influencing factors of carbon at critical interfaces, including atmosphere-vegetation, soil-atmosphere, soil-rock, and rock-water systems. A forward-looking research framework integrating multi-source data and process-based modeling was proposed to clarify the carbon quantification characteristics across different interfaces of karst systems, reveal the differences in multi-interface carbon fluxes and their underlying mechanisms, and provide theoretical references for studying carbon dynamics in heterogeneous karst environments. It also offers critical theoretical support for scientifically evaluating the carbon sink capacity of karst systems and advancing the development of carbon sink enhancement technologies.

Conclusions The proposed methodological system offers a reference framework for studying the migration and transformation of carbon across multiple interfaces-atmosphere-vegetation-soil-rock-water and establishes new approaches and tools for accurately quantifying carbon sink characteristics in rocky desertification areas. It provides a scientific basis for interpreting karst carbon cycle processes and carbon migration pathways, helping to uncover the fate of the "missing carbon sink." The study will provide a scientific foundation for ecosystem restoration and sustainable development strategies in karst regions.