Agricultural intensification (AI) has significantly altered soil ecosystems, affecting microbial community structure and function, which are crucial for soil fertility and ecosystem stability. This study investigated the responses of soil microbial communities (bacteria, fungi, archaea) to different AI levels (conventional farming, intensive farming, and organic farming) in three agricultural regions across the Northern Hemisphere. High-throughput sequencing and functional prediction revealed that AI significantly reduced microbial alpha diversity, shifted community composition, and altered functional gene abundances related to nutrient cycling and organic matter decomposition. Specifically, intensive farming increased the relative abundance of copiotrophic bacteria while decreasing that of oligotrophic bacteria and ectomycorrhizal fungi. Additionally, soil physicochemical properties (pH, organic carbon, total nitrogen) were key drivers of microbial community changes. Organic amendments and crop rotation were effective in mitigating the negative impacts of AI on microbial communities. This study provides insights into the mechanisms underlying microbial responses to AI and offers practical strategies for sustainable agricultural management.