<p>Fungal-bacterial co-culture systems have attracted increasing attention for their enhanced efficiency in volatile organic compounds (VOCs) biodegradation. This review provides a molecular-level overview of the mechanisms underlying metabolic enhancement in co-culture systems. First, the representative fungal and bacterial strains used to construct co-culture systems were introduced, and the key operational parameters influencing their performance were discussed. Second, the microbial interaction mechanisms within co-culture systems, including interspecies signaling, metabolic cooperation, substrate exchange, and ecological niche differentiation, were analyzed. These interactions collectively support the functional stability of fungi and bacteria and the degradation efficiency of VOCs. Third, the bidirectional effects between VOCs and co-cultured microorganisms were summarized, focusing on metabolic responses, stress adaptation, and community restructuring under VOCs exposure. Finally, key challenges were identified, such as the instability of metabolic synergy and the limitations of current synthetic biology tools, highlighting the need for omics-based analysis and dynamic regulatory strategies. This review offers theoretical guidance for the rational design and optimization of fungal-bacterial co-culture systems in VOCs biodegradation.</p> Graphical abstract <p></p>