In aquatic benthic environments, benthic organisms have been found to regulate important biogeochemical characteristics and perform key ecosystem functions. To further explore the ecological impact of the snail 's, presence on the benthic environment, we employed high-throughput sequencing technology to investigate its effects on the bacterial, fungal, and protist communities in sediment and their intrinsic interactions. Our findings revealed that 's presence significantly enhanced the diversity and evenness of the fungal community while simultaneously decreasing the diversity and richness of the protist community, and it also altered the composition and relative abundance of the dominant phyla across the bacterial, fungal, and protist communities. The snail considerably altered the co-occurrence networks of the microbial communities, particularly by enhancing the intrinsic complexity of the protist community and by strengthening the interconnections among the protist, bacterial, and fungal communities. Notably, the proportions of specialists within the sediment bacterial, fungal, and protist communities declined due to the snail . Its presence also notably expanded the habitat niche breadth for sediment bacteria and protists. In terms of community assembly, shifted the fungal community assembly from being dominated by stochastic processes to being dominated by deterministic processes, whereas the protist community assembly shifted from deterministic processes to being dominated by stochastic processes. The mainly altered ecological processes in the fungal and protist assemblies were drift and homogenizing selection. Additionally, the presence of resulted in a notable reduction in the sediment ON level and a significant increase in the ammonia, FA, and EN concentrations. Sediment properties, particularly FA and nitrate, were strongly correlated with microbial communities and were key contributors to changes in microbial community dynamics. These research findings not only broadened our understanding of the ecological impacts of on benthic microbial communities but also highlighted its substantial potential in enhancing microbial community stability.