Soil organic carbon (SOC), especially the stable SOC, have the important ecological function in the carbon cycle. As a typical stable SOC, soil phytolith-occluded organic carbon (PhytOC) is one of the important mechanisms of long-term soil carbon sink in terrestrial ecosystems. However, the distribution characteristics, accumulation law, and cycle process of soil PhytOC in fragile karst ecosystems are still not cognized. The purpose of the present study is to obtain the distribution pattern and change law of total SOC and soil PhytOC in different land cover types and to clarify the influencing factors and driving mechanism of land cover change on total SOC and soil PhytOC content and storage in the karst ecosystem. In the typical karst area of Southwest China, five representative land cover types, including bamboo forest (BF), coniferous and broad-leaved mixed forest (CBF), shrub (SH), grassland (GL), and agricultural abandoned land (AAL), were selected as the research objects. The total SOC contents, soil PhytOC contents, and soil physical and chemical properties were determined in the lab. Soil PhytOC and total SOC storage were calculated by the formulas. Data were analyzed statistically by linear regression, Pearson correlation analysis, LSD multiple comparison, and principal component analysis. Land cover change can affect obviously total SOC and soil PhytOC content and storage in the karst subtropical forest. Among the five land cover types, soil phytolith content, soil PhytOC content and storage, and total SOC storage of each soil profile in the BF were all significantly higher than those of the other four land covers. Among the three different soil profiles of 0~10, 10~20, and 20~30 cm, total SOC and soil PhytOC contents of the surface soil layer in the five land cover types were all the most, and the content decreased obviously with the increase of soil depth. There were significant positive correlation between the contents of soil available silicon, phytolith, and PhytOC. Soil available silicon content, soil phytolith content, and soil C/N were significantly positive related with the accumulation of total SOC and soil PhytOC. Soil PhytOC content or storage was significant or extremely significant related with total SOC content or storage. The results of the present study provided scientific bases for further evaluating the carbon sink capacity of soil PhytOC in the karst ecosystem, in SW China, and have important values in the reduction of carbon emission and increase of carbon sink to combat the global warming. In addition, the results of the present study also can provide theoretical references for the vegetation restoration of karst rocky desertification in Southwest China.