Karst ecosystems are important landscape types that cover about 12% of the world’s land area. The role of karst ecosystems in the global carbon cycle remains unclear, due to the lack of an appropriate method for determining the thickness of the solum, a representative sampling of the soil and data of organic carbon stocks at the ecosystem level. The karst region in southwestern China is the largest in the world. In this study, we estimated biomass, soil quantity and ecosystem organic carbon stocks in four vegetation types typical of karst ecosystems in this region, shrub grasslands (SG), thorn shrubbery (TS), forest - shrub transition (FS) and secondary forest (F). The results showed that the biomass of SG, TS, FS, and F is 0.52, 0.85, 5.9 and 19.2 kg m22 , respectively and the corresponding organic cabon storage is 0.26, 0.40, 2.83 and 9.09 kg m22 , respectively. Nevertheless, soil quantity and corresponding organic carbon storage are very small in karst habitats. The quantity of fine earth overlaying the physical weathering zone of the carbonate rock of SG, TS, FS and F is 38.10, 99.24, 29.57 and 61.89 kg m22 , respectively, while the corresponding organic carbon storage is only 3.34, 4.10, 2.37, 5.25 kg m22 , respectively. As a whole, ecosystem organic carbon storage of SG, TS, FS, and F is 3.81, 4.72, 5.68 and 15.1 kg m22 , respectively. These are very low levels compared to other ecosystems in non-karst areas. With the restoration of degraded vegetation, karst ecosystems in southwestern China may play active roles in mitigating the increasing CO2 concentration in the atmosphere.