Soil organic carbon (SOC) pool plays a key role in the terrestrial eco-systems. Limited by the map scale of soil maps, the linkage between attribute and spatial data can cause large uncertainties in estimating SOC storage with the soil type method. In this study, with a total of 798 SOC density data and the 1:500 000 soil maps, the SOC storage in Yunnan-Guizhou-Guangxi Region of China (including Yunnan province, Guizhou province and Guangxi Zhuang Autonomous Region) was estimated using the soil type method with the linkage of arithmetic mean method, median method, and area-weighted mean method (based on the area recorded in the Soil Series) based on different map units and the results were compared with that of the linkage of PKB method (Pedological Professional Knowledge Based Method). The results show that the linkage of area-weighted mean method is better than arithmetic mean method and median method. The differences of the estimates with area-weighted mean method based on different map unites are the smallest. The PKB method can do better when the detailed soil maps with large map scales are utilized, or else the area-weighted mean method should be adopted.