Abstract:[Background] As an important energy resource, coal is in high demand in production activities. However, long-term coal mining causes serious damage to the eco-environment. Microbial remediation, as an environmentally friendly, simple, and low-cost remediation method, has broad application prospects in the restoration of coal mining areas. [Objective] We used a composite microbial agent for the remediation of spoil sites in coal mining areas, aiming to restore the fragmented eco-environment of coal mines through microbial activities and interactions of microorganisms with plant roots. [Methods] Utilizing 16S rRNA gene high-throughput sequencing, we analyzed the microbial community structure at the remediation site. By monitoring the soil nutrient content, heavy metal concentrations, and growth of buckwheat plants, we assessed the efficacy of microbial remediation and explored the functions of the microorganisms. [Results] There were diverse microbial species with remediation capabilities at the experimental area. The addition of the microbial agent reduced the microbial diversity but had a minor impact on the indigenous microbial community structure at the experimental site. The on-site restoration for 150 days increased the organic matter, total nitrogen, total potassium, available nitrogen, available phosphorus, and available potassium by 70%, 20%, 48.4%, 40%, 26.8%, and 24.2%, respectively, which indicated the significant recovery in soil fertility. The organic matter, available phosphorus, and available potassium showed an increasing trend during the restoration period, indicating that functional microorganisms continuously provided efficient nutrients for plant growth. The decrease of 49% in arsenic and 41% in copper indicated that microorganisms played a role in the remediation of heavy metals at the site. Microorganisms promoted the growth of plant roots, enhancing the absorption and utilization of nutrients by plants. They increased the buckwheat plant height, dry weight, and crude protein content by 30%, 100%, and 22.4%, respectively. [Conclusion] The microbial agent significantly improved the soil fertility, suppressed the toxic effects of heavy metals in the soil, and promoted the growth of economic crops at the experimental site. Microbial remediation holds a great application value in the restoration of fragmented ecosystems in coal mining areas.