Soil organic carbon (SOC) is the dynamic medium of carbon transfer and the main way of carbon circulation in karst ecosystem, SOC and soil labile organic carbon (LOC) is essential for karst soil C cycling. There has been very little research about the differentiation of SOC and LOC in karst ecosystem. In this study, six typical restoration measures were investigated in the karst rocky desertification ecosystem, southwest China, including: restoration with Zanthoxylum bungeanums (HJ), restoration with Hylocereus undulates (HL), restoration with Pennisetum sinese (HZ), restoration with Medicago sativa (MX), restoration with Sabina chinensis (YB), and abandoned and natural recovery (LH). The SOC contents, SOC stocks, LOC contents (water soluble organic carbon (WSOC), easily oxidizable organic carbon (EOC), particulate organic carbon (POC), light fraction organic carbon (LFOC)), and the carbon pool management index (CPMI) were investigated. The results indicated that the SOC contents, SOCS and LOC contents of the six measures were the highest in YB, followed by the LH, and the two were significantly higher than the other four measures. The soil CPMI contents of 0-20 cm layer under the different restoration measures decreased in the following order: YB > HJ > MX > HL > HZ. Correlation analysis showed that SOC was positively correlated with soil LOC (P<0.01), and LOC was positively correlated with each other (P<0.01). These findings suggest that restoration with Sabina chinensis, abandoned and natural recovery are more conducive to the management and protection of karst ecological environment. Restoration with Zanthoxylum bungeanums can be used as a priority economic species for karst rocky desertification and mountain agricultural development in southwest China. Soil WSOC, EOC, POC, and LFOC can be used as effective indicators to reflect SOC pools, and soil CPMI can also be used as a sensitive indicator to reflect soil management.