White-nose syndrome, caused by the psychrophilic fungus Pseudogymnoascus destructans, is a wildlife disease that infects hibernating bats, resulting in the deaths of millions of bats in North America. Previous studies have confirmed that volatile organic compounds (VOCs) effectively inhibit the growth of P. destructans, but the antifungal mechanisms of these compounds have not been comprehensively characterized. This study screened two VOCs, 2,5-Dimethylcyclohexanol (DMCH) and nonanal, identified from bat cave environments for their potent inhibition of P. destructans. Scanning and transmission electron microscopy revealed mycelial deformations and disruptions in cellular structures following treatment with these compounds. Physiological and biochemical analyses showed that the VOCs induced mycelial apoptosis, increased reactive oxygen species (ROS) activity, increased adenosine triphosphate (ATP), superoxide anion, and glutathione (GSH) contents, and decreased catalase (CAT) and superoxide dismutase (SOD) activities. Comprehensive transcriptomic and metabolomic analyses revealed that the VOCs disrupted mycelial cell wall and membrane structures, affected the expression of virulence genes, interfered with basic metabolic processes, led to disorders in energy metabolism, induced oxidative stress with ribosomal overexpression, interfered with the MAPK signaling pathway, and ultimately induced cell apoptosis. This study provides novel insights into the antifungal effects of VOCs targeting P. destructans and offers a scientific basis for combating white-nose syndrome.