Postharvest Flammulina filiformis is prone to quality degradation, adversely impacting its commercial value. Cordyceps militaris, rich in antioxidant and antibacterial components, shows promise as a natural biological preservative. This study aimed to explore the potential of C. militaris extract (CME) as a preservative for F. filiformis. Through analyzing indicators such as browning, stipe elongation, and cap diameter, this study confirmed the effectiveness of CME in delaying oxidation and inhibiting microbial growth during storage. Additionally, transcriptome analysis revealed that CME modulated gene expression in F. filiformis, enhancing its antioxidant defense mechanisms. The results demonstrated that CME could effectively extend the shelf life of F. filiformis, providing valuable insights into preservation strategies for this and other edible fungi.