Microorganisms, as the foundation of deep-sea ecosystems, are crucial for maintaining the structure and stability of polymetallic nodule field environments. To investigate the community structure and distributional patterns of benthic microorganisms in such environments, this study used high-throughput sequencing to analyze the composition, diversity, and environmental correlations of bacteria, archaea, and fungi in the BPC (Beijing Pioneer Hi-tech Development Corporation Ltd., Beijing, China). Furthermore, microbial communities from BPC were compared with those from UK-1 (UK Seabed Resources, Southampton, UK) in terms of community structure and co-occurrence network characteristics. The results revealed that in the BPC, the bacterial communities were dominated by Proteobacteria and Chloroflexi, while Crenarchaeota represented the overwhelmingly dominant group. Fungal communities were primarily composed of Ascomycota and Basidiomycota. Correlation Analysis suggested that water depth, TOC (Total organic carbon), TN (Total nitrogen), and δ¹⁵N emerged as the key environmental drivers of microbial community variation. Comparative analysis showed microbial groups exhibited certain similarities but also some differences at the phylum, class, and order levels, with the differences becoming increasingly pronounced at finer taxonomic resolutions between BPC and UK-1. Co-occurrence network analyses indicated the microbial networks with higher density and node connectivity in the BPC, whereas the UK-1 exhibited greater modularity and clustering coefficients. Microbial interactions were weaker in the UK-1, but its resilience to benthic disturbance was expected to be higher than in the BPC.