Determining the relationship between soil microbial populations and soil microbial biomass in ecosystems can provide useful information for vegetation restoration in the canyon Karst region. Therefore, based on a combination of field investigation and laboratory analysis, we analyzed soil microbial populations and soil microbial biomass at different soil depths as well as their fractal relationships under six typical ecosystems, i.e., paddy field, dry land, grassland, Shrubbery, plantation forest, and secondary forest, in the canyon Karst region in southwest China. Three plots with size of 20 m × 20 m were constructed in each ecosystem type, and five soil samples were collected at four corners and the middle in each plot and then mixed as one sample. The dilution plate method and the chloroform fumigation extraction method were used to determine soil microbial populations and soil microbial biomass., respectively. The results showed that soil microbial populations and composition varied under different ecosystems in the canyon karst region. Soil microbial populations were largest in the secondary forest, followed by the plantation forest, while least in the dry land, indicating that the project of returning crop land to forests or grassland have a significant impact on increasing the soil microbial populations. Microbial composition in the six ecosystems performed in the order of bacteria > actinomycetes > fungi. The bacteria number was 26.66×10⁵-71.64×10⁵cfu/g with the highest proportion of 87.00%-95.50% of total soil microbial number; followed by actinomycetes, whose number and proportion were 1.45×10⁵-3.78×10⁵cfu/g and 4.21%-12.39%, respectively. However, the fungi quantity was 0.07×10⁵-0.23×10⁵cfu/g, and the proportion was less than 1%, just only 0.24%-0.61%. Under different ecosystem types, soil microbial biomass carbon (MBC), soil microbial biomass nitrogen (MBN), and soil microbial biomass phosphorus (MBP) were diverse, but all of them appeared to be a trend of MBC > MBN > MBP. Soil MBC and MBN was highest in the secondary forest, while MBP was highest in the plantation forest, in comparison with that MBC was lowest in the dry land, MBN and MBP were lowest in the grass. The ratios of MBC/SOC, MBN/TN and MBP/TP ranged from 0.44%-0.97%, 2.13%-3.13%, and 1.46%-2.13%, respectively, with no significant differences among the six ecosystems. The value of MBC/MBN ranged from 3.06 to 6.54, which in the secondary forest was significantly higher than that in other ecosystems; however, no significant differences existed among the rest ecosystems. A good fractal relationship existed between soil microbial populations and soil microbial biomass at a highly significant level (P < 0.01). Moreover, both soil microbial populations and soil microbial biomass in the six ecosystems decreased as an increase in soil depth. As a result, exploring soil microbial activities could provide the basis for improving the soil fertility of lime soil and boosting vegetation restoration in karst regions.