Soil samples were collected from three different types of underground root habitat typical of Karst area (Type I-dolomite of low oblique occurrence with multilayer space, Type II-dolomite of middle oblique occurrence with multilayer space and Type III-dolomite of high oblique occurrence with multilayer space types), for analysis of enzyme activity in the soils as affected by type of underground root habitat and level of soil layer, and correlation between soil enzyme and soil nutrients content. Results show that: 1) soil enzyme activity varied sharply between different habitat types and between different spatial soil layers(p<0.01). 2) Type I is conductive to cycling of soil carbon, Type II to transformation of N-containing compounds and Type III to oxidation of soil organic matter, and moreover, soil enzyme activity in all the three types decreased with soil depth. 3) soil enzyme activity was significantly related to soil nutrients content. So their correlation coefficient can be used as an indicator for evaluation of soil quality/fertility. Obviously, the finding of differences between the types of root underground habitat in soil enzyme activity may be very useful to evaluation of soil quality, study on technology for vegetation restoration and ecological remediation and management in the Karst rocky desertification region.