To develop new methods for transforming waste resources such as landfill leachate and weathered coal into clean energy, this research analyzed the co-fermentation effect and internal mechanism of methane production through gas chromatography, three-dimensional fluorescence, inducive coupling and metagenomics techniques. Our findings revealed that landfill leachate addition drives more than 70% increase in weathered coal biomethane production. Anaerobic fermentation collectively increased the tryptophan content in liquid-phase biodegradation, with the highest proportion reaching up to 72%. Paracoccus, Ralstonia, Aquamicrobium and other major microorganisms were in the range of 9–32%. Contamination of heavy metal diversity resistance genes has impacted microflora composition, with specialized heavy metal resistance genes such as NreB, CopD, NreB, and MerP altering the influence of heavy metals on anaerobic fermentation. The combined anaerobic fermentation of landfill leachate and weathered coal has expanded clean waste utilization and has broad application prospects.