Reforestation serves as one of the most effective strategies for mitigating global warming, but a comprehensive understanding of its impact on soil microbial biogeochemical cycling functions remains lacking. In this study, we collected paired reforested and cropland soils from 30 sites in the southwestern China to comprehensively investigate the impacts of reforestation on soil microbial functional genes related to carbon, nitrogen, and phosphorus cycling. Microbial diversity, functional profiles, and functional gene copies were determined through amplicon sequencing, metagenomic analysis, and real-time PCR. We found that reforestation significantly decreased the average copy number of the 16S rRNA operon and altered the soil microbial community structure. Reforestation also substantially increased the abundances of most microbial functional genes involved in carbon (e.g., carbon degradation and fixation), nitrogen (e.g., nitrogen fixation, ammonia oxidation, and denitrification), and phosphorus (e.g., inorganic phosphorus solubilization, organic phosphorus mineralization, and phosphorus transportation) cycling. The carbon, nitrogen, and phosphorus cycling gene abundances were significantly correlated with multiple environmental factors, including soil moisture, total nitrogen, total carbon, and NH4+-N, in both cropland and reforested ecosystems. Notably, they showed significant correlations with the soil available potassium and NO3−-N contents specifically within the reforested soils rather than the cropland soils. Additionally, reforestation substantially simplified the co-occurrence network constructed with soil microbial carbon, nitrogen, and phosphorus cycling genes. The results collectively indicate that reforestation can substantially enhance soil microbial biogeochemical cycling functions but reshape their co-occurrence pattern, providing critical information for assessing the ecological impacts of reforestation projects on ecosystem health.