<p>Metal elements in soil are important factors that affect crop yield and quality. As organic manures, the application of green manures can improve soil quality and crop yield. However, there are still insufficient studies on the effects of soil quality improvement, elemental content changes and microbial community changes under multi-year green manure intercropping. This study aims to explore the effects of multi-year green manure intercropping, and further explore the relationship between microbial community and metal element content. In this study, data pertaining to soil properties, enzymatic activities, and maize yield were collected. The metal content was measured using ICP-OES in this study, and the microbial groups were classified based on metagenomic to explore their correlation. The results revealed that intercropping of green manure for many years was beneficial to increase maize yield. Multi-year intercropping increases maize yield by improving soil quality, regulating element content, and influencing microbial communities. Multi-year green manure intercropping had a significant effect on soil elemental content, increasing the content of Ca, Ca, Mg, Al, and Fe, and decreasing the content of Pb and Mn. Multi-year intercropping with green manure contribute positively to soil quality improvements, including enhancing soil carbon sequestration and accumulation, reducing soil bulk density, and elevating soil alkaline enzyme activity. The microbial community has a significant positive impact on Ca, Mg and Al contents, and a significant negative impact on Pb and Mn contents. And there are 30 genera could be used as potential biomarkers to predict changes in soil metal element content.</p>