Abstract: The synergistic symbiosis of microbial communities plays an irreplaceable role in maintaining ecosystem functional stability. In coal reservoirs, microbial degradation of organic matter is a multi-step metabolic process accomplished through the collaboration of diverse microorganisms. The theory and technology of "Coalbed Methane Bioengineering" can be applied to enhance coalbed methane well production while achieving carbon-negative emission effects. Therefore, in-depth research on the functional potential and symbiotic relationships of microbial communities in coal reservoirs is crucial for CO₂ resource utilization. Focusing on microorganisms involved in carbon metabolism and biogeochemical cycling within the aqueous environment of the No. 3 coal seam in the southern Shizhuangnan Block of the Qinshui Basin, this study employed metagenomic sequencing and symbiotic network analysis to investigate the spatiotemporal evolution of microbial community structure, diversity, and collaborative metabolic potential in subsurface in-situ environments. Results show that Bacterial community structures in the coal seam aqueous environment exhibited greater seasonal or groundwater runoff sensitivity compared to archaeal communities. Microorganisms participated comprehensively in carbon metabolism and biogeochemical cycles, with widespread C-N-S-Fe cycle genes associated with organic matter degradation, methanogenesis, and sulfate reduction. Seasonal and regional variations in reservoir geochemical environments, influenced by external water recharge and runoff conditions, determined spatiotemporal heterogeneity in microbial metabolic functional potential. Microbial consortia carried more organic degradation-related genes during non-rainy seasons, while the correlation between metabolic functions and geochemical factors weakened during rainy seasons. Ecosystem stability and sustainability in in-situ reservoir environments depend not only on microbial diversity and metabolic functions but also on their synergistic relationships. Complex microbial interactions and symbiotic networks facilitate organic degradation and biogeochemical cycling of bioessential elements. This study provides theoretical foundations and practical guidance for CO₂ biomethanation in organic reservoirs and production enhancement through “Coalbed Methane Bioengineering”.