Karst region is a typical ecological fragile zone, with small environmental and anti-interference capability. Many environment factors, such as different land use, elevation and topographic relief, have significant influence on spatial variability of soil properties, resulting in abnormal fragments of landscape and severe rocky desertification. The method of canonical correspondence analysis (CCA) was employed to reveal the relationships between soil and environment in peak-cluster depression areas of karst region, using the samples from field survey in Guzhou. Results show that spatial variability of TN, AN, SOC, AP, AK and C/N are greater than TP, TK, and pH, with the similar trend among TN, AN and SOC. Furthermore, CCA shows that SOC, TN and AN have high correlation with bare rock rate and grade, AK and vegetation type, together with the significant correlation between C/N and soil depth, while the environment has little effect on TK, TP and pH. Environmental factors that affect soil properties are listed as the following order: land use > vegetation type > bare rock rate > aspect > soil depth > elevation. Except TK and pH, soil properties are significantly affected by different land-use types.