The main soil nutrients, soil mineral nutrients, and soil microbes were investigated, sampled, and analyzed in farmland, grassland, scrub, plantation forest, secondary forest, and primary forest in depressions between karst hills. Multiple comparison analysis, principal component analysis, and canonical correlation analysis were used to study the soil characteristics and the main factors affecting soil fertility as well as the relationships between those three factors: the main soil nutrients, soil mineral content, and soil microbes. Soil pH ranged from 6.60 to 7.75 in depressions between karst hills. Across the different ecological systems, from farmland to primary forest soil, pH varied from acidic to alkaline. The soil nutrient content varied in different ecological systems, and changes in soil nutrient content can be modeled during the process of ecological succession. In the process of secondary succession soil organic matter (SOM), total nitrogen (TN), total phosphorous (TP), available nitrogen (AN), and available phosphorous (AP) content increased gradually. The soil nutrient levels were highest in primary forest and follow the sequence of primary forest > secondary forest > shrub > grassland. The soils of these habitats were all significantly or very significantly different. When the landuse type was changed from a landscape with natural secondary succession to farmland or plantation forests, soil TP and TK content increased significantly. The content of the main soil nutrients (SOM, TN, TP, TK, AN, AP, AK), microbial populations, and the soil content of C, N, and P in microbial biomass (C_mic, N_mic, P_mic, respectively), were obviously higher in the karst area than that in the red soil region at the same latitudes. The content of mineral nutrients was relatively low and the sum of SiO₂, Al₂O₃, and Fe₂O₃ accounted for more than 90% of the total mineral nutrients. Although the supply of Ca and Mg were adequate, serious shortages of other mineral nutrients limited plant growth and development. Many types of ecological systems in depressions between karst hills were not obviously showing signs of rocky desertification, although a strong potential for rocky desertification still exists. All ecosystems studied here had high soil microbial populations, and primary forest had highest total microbial populations, bacteria populations and Actinomyces population while plantation forest had the lowest. Soil fertility can be ranked in the order of primary forest > secondary forest > scrub > grassland > farmland > plantation forest. The landscape in this karst area is strongly heterogeneous; the ecological systems are complex because numerous factors affect the ecosystems and different ecological systems are influenced by different factors. Therefore, the practice of returning farmland to forests or grassland tends to improve the soil ecosystem environment in karst areas which have undergone rocky desertification. Farmland requires more organic and nitrogenous fertilizers and plantation forests require more nitrogenous fertilizer than other ecosystems. In the primary forest, plants and soil nutrients reach a state of dynamic equilibrium, and land management should focus on strengthening and improving the forest environment and balancing the relationships among plants, soil nutrients and microbes. Assuring that soil resources are used rationally will be helpful in improving the results of ecological restoration and accelerate vegetation rehabilitation in depressions between karst hills or even in the entire karst region of southwest China.