Although agricultural land abandonment (LA) is accompanied by land degradation, it could be considered a kind of self-rehabilitation. Studies have shown that long-term LA has profound ecological and environmental benefits, whereas few studies have compared LA with human intervention (HI), which involves planting and fertilization in agroecosystem restoration. Here, we established four different scenarios based on local livestock husbandry, including LA without HI, LA with slight human intervention (HIS), medium human intervention (HIM), and intensive human intervention (HII). LA experiments were conducted for 3 years and repeatedly sampled three times. The soil bacterial and fungal communities were determined to present the ecological impacts. In this study, LA and HIS could save soil inorganic carbon and total calcium (Ca) contents and benefit soil mycorrhizal fungi and plant growth-promoting rhizobacteria. LA and HIM benefited some microbial communities associated with complicated organic compounds. Human interference methods did not significantly increase soil nutrients after 3 years of farmland abandonment. However, indigenous vegetation increased the risk of plant diseases based on soil microbial communities. Forage grass may control the risk, and HIS was a cost-effective scenario in our study. Moreover, we should maintain a cautious attitude toward HII to prevent excessive intervention.