Carbon sink processes related to the weathering of silicate minerals are often accompanied by physical, chemical, and biological effects. In particular, plant-microbe synergistic effects are important for soil mineral weathering, but relevant correlation analyses and quantitative studies remain sparse. In this research, a standard serpentine test specimens (STSs) with specific specifications were used to study serpentine weathering under different environmental conditions (abiotic or biotic) and correlated it with the microbial community structure under the growth of Setaria viridis. The results showed that the environment with growing S. viridis had the strongest weathering capacity for STSs, which was 35 times higher than that of the abiotic environment group, and a significant increase in soil inorganic and organic carbon contents compared with the abiotic environment and the environment without plant growth. The bacteria with strong weathering ability were enriched in the soil of around STSs, such as Pseudomonas spp. and Sphingomonas spp. In addition, the fungal community of Ascomycetes is also heavily enriched, accelerating STSs weathering. The addition of bacterial agent (Bacillus subtilis) further promoted the STSs weathering under the growth conditions of S. viridis. The soil surrounding the buried STSs was also enriched with heavy metal tolerant Massilia spp. and disease suppressing Lysobacter spp., while the abundance of fungi functionally associated with pathotypes was reduced, thereby benefiting plant growth. This study provides basic information for the serpentine bio-weathering coupled with carbon sequestration by using plant-microbe synergistic effects.