The distribution of the contents of soil carbon and nitrogen were explored in seven kinds of micro-habitats (earth flatland, rocky flatland, stone crevice, stone gully, stone cavern, stone groove and stone pit) under different vegetation types (shrub, forest and grassland) in karst region of south western China. The results showed that organic carbon and total nitrogen contents in top soils varied from 10.6 to 103.7 g/kg and from 1.16 to 6.39 g/kg respectively in study area. Distribution of the contents of soil carbon and nitrogen were obvious different under different vegetation types. As to forest, the average contents of soil carbon and nitrogen were doubled 100% more when compared with grassland; as to shrub, the spatial variability of the contents of soil carbon and nitrogen were small. The contents of soil organic carbon and nitrogen were normally distributed under different vegetation types, while the contents of organic carbon and total nitrogen showed right-skewed distribution. The contents of soil organic carbon and total nitrogen were higher in relatively open habitats (earth flatland, rocky flatland, stone crevice and stone pit) than the others. The correlations between the contents of soil organic carbon, total nitrogen, alkaline hydrolytic nitrogen, Olsen-P and carbon nitrogen ratio were significantly correlated in same vegetation type.