White-rot fungi have received widespread attention owing to their strong ability of lignocellulosic degradation. However, research on applying white-rot fungal to alter coal (lignin-like polymers) for hydrogen production is scarce, also the related mechanism is unclear. In this study, white-rot fungi were utilized to decompose the high volatile bituminous coal. The results showed that hydrogen production from anaerobic digestion (AD) of white-rot fungi pretreated coal (C3) was accelerated, the total hydrogen production was 20.3 times AD of coal (C4). It was attributed to C3 had a higher hydrogenase activity, lower acidity and more stable reducing environment than C4, resulting in more intermediates, such as alkanes, acids/alcohols, and esters. Additionally, fungal pretreatment enhanced the competitiveness of the important hydrogen synthetic Clostridium, the relative abundance remained at about 21.0% compared with other bacterial communities. Finally, the study evaluated the benefit of this strategy from economic and environmental perspective, as well as a preliminary analysis of field application. It illustrated that C3 significantly reduced the CO content in flue gas, which was 28.7% lower than coal (C1) in flue gas from coal combustion and showed an approximate 20.1 times C4 in terms of output.