Vegetation restoration plays a critical role in terrestrial carbon sink increase, especially in subtropic Southwest China which has been the hotspot of vegetation restoration areas in recent decades. However, the variations in microbial community diversity resulting from this intervention remain unclear, and further research is needed to elucidate the complex interactions between microorganisms and soil nutrient elements. Soil samples were collected from three vegetation restoration stages in a karst rocky desertification (KRD) valley of Southwest China, which were named dry cropland (CL), 3–8 years grassland (WL), and afforestation land that recovered more than 20 years (AL), to investigate the soil nutrient and bacterial diversity variation during vegetation restoration course. The soil organic carbon (SOC) and total nitrogen (TN) contents are significantly higher in the afforestation land soil compared to the cropland and grassland soils, while the available nutrient contents decrease during the vegetation restoration course. The soil dominant bacteria genus shifts from R-strategy bacteria in cropland to K-strategy bacteria in afforestation land, and the relative abundances of R-strategy genera remain similar in the grassland and cropland soil. The dual-relative bacteria network evaluates from simple correlation net to very complex ones during the vegetation restoration, of which the core influenced factor alters from available nutrients to organic matter. The results of this study suggest that it will take a relatively longer period for the soil nutrient conditions and bacterial community to recover fully, although vegetation restoration could reduce the impacts of agricultural activities. This study refers to the ecological preservation and restoration strategies under the global climate change background, elucidating the nutrient metabolism variation induced by the accordance variation of organic matter accumulation and soil bacterial life strategy during the ecosystem restoration course.