Oysters are one of the largest marine shellfish species worldwide. However, oyster shells are treated as waste, accumulating on coastal shores and seriously polluting the ecosystem. In this study, a composite microbial agent was developed using calcined oyster shell powder, Beauveria bassiana spore powder, and ecological chitosan. To release the active ingredients, oyster shells were treated by calcination. The optimal application ratio of the agent was determined by detecting tomato growth indicators. Application of the optimized agent to vineyards increased 100-grain weight, carotenoids, and total amino acids by 10.55%, 8.71%, and 29.40%, respectively. Further detection of soil microbial population changes showed that the application of the agent increased the abundance and diversity of soil microbial populations, promoting the metabolism of bacterial amino acids, polysaccharides. These findings suggest that the agent not only enhanced plant growth and fruit quality, but also enriched the diversity and abundance of soil microbial communities.