Abstract: Weathered coal has low calorific value, single utilization mode and environmental pollution. In order to broaden the utilization way of weathered coal, realize resource utilization and environmental protection, dark fermentation of weathered coal was carried out to produce biological hydrogen. Naturally weathered coals from three mining areas of Jincheng and Taiyuan in Shanxi Province and Wuhai in Inner Mongolia were selected, and the coal seam mine water was used as the source of bacteria. The feasibility of biological hydrogen production from weathered coal and the key metabolites and pathways were revealed by means of biological hydrogen production test, GC-MS, three-dimensional fluorescence and metagenomics. The results show that weathered coal in different mining areas can be converted into bio-hydrogen, and the hydrogen production of Wuhai weathered coal is the largest (10.26 mL/g), which is much higher than that of Jincheng weathered coal (5.22 mL/g). The hydrogen production system of weathered coal is in an acidic environment, and pH and COD mass concentration have certain regular changes. In the process of hydrogen production from weathered coal, the liquid organic matter is mainly composed of acids (acetic acid, propionic acid, valeric acid and butyric acid) and alcohols (2,3-butanediol, sugar alcohol and (S)-1,2-propanediol). The soluble organic matter is mainly composed of humic acid and tryptophan protein organic matter, and with the progress of fermentation, a variety of organic matter is consumed and utilized. In the process of hydrogen production from weathered coal, microorganisms are mainly dominated by Pseudomonadota and Citrobacter, and hydrogen is mainly produced by decomposing and utilizing organic acids (acetic acid, propionic acid, butyric acid, lactic acid). In the process of hydrogen production from weathered coal, the acetic acid metabolic pathway is dominated by the glycolysis pathway. The organic matter is decomposed by bacteria to produce pyruvate and then used by hydrogen-producing bacteria. Among them, alanine kinase and aldehyde ketone dehydrogenase play an important role in the process of cell metabolism to produce hydrogen. The research results reveal the potential mechanism of hydrogen production from weathered coal and provide a theoretical reference for the effective utilization of weathered coal.