Microbial transformation of dissolved organic matter (DOM) is a central process in subsurface carbon cycling, yet its long-term dynamics in shale environments remain poorly constrained. We conducted an 810‑day incubation experiment using DOM leached from immature Cretaceous marine black shale to investigate fluid–rock–microbe interactions and their role in climate‑active gas generation. Liquid chromatography–organic carbon detection (LC‑OCD) revealed progressive microbial degradation of labile DOM pools and the accumulation of recalcitrant fractions, accompanied by sustained CO₂ and CH₄ release. These findings demonstrate that shale DOM can fuel persistent microbial metabolism, restructure DOM composition, and contribute to subsurface carbon fluxes over extended timescales. Our results highlight the ecological significance of shale DOM biodegradation in unlocking deep carbon reservoirs and provide new insights into the microbial mediation of subsurface biogeochemical cycles.