Microbial consortium degradation technology can improve the degradation efficiency and adaptability through fungi-bacteria synergism, but the mechanism of the fungi-bacteria interaction is still unclear, making it difficult to optimize the degradation process. The microbial consortium J-6, with high lignin degradation efficiency and strong environmental adaptability, was obtained in our previous research. In this study, the fungi-bacteria interacting mechanism of the microbial consortium J-6 was inferred based on metabolomics technology. The results showed that the positive interaction between fungi and bacteria could improve the efficiency of lignin degradation. The metabolites released by fungi, especially betanidin and ergosterol, had an impact on bacterial metabolism, promoted the degradation of macromolecules, and significantly increased the lignin degradation efficiency. Metabolites released by bacteria, especially L-phenylalanine and taurine, played a key role in fungal metabolism, leading to more complete degradation. The interaction mechanism of chemical currencies exchange between fungi and bacteria during lignin degradation obtained in this study can provide theoretical guidance for microbial consortium degradation technology.