Flammulina velutipes was treated with 10, 50, and 250 μL L−1 isoamyl isothiocyanate (IAITC), and effects on quality preservation were assessed. IAITC displayed positive effects during the storage of F. velutipes: (i) maintained tissue integrity, reduced weight loss rates; (ii) reduced browning degree by inhibiting the activities of browning-related enzymes; (iii) enhanced activities of two antioxidant enzymes (superoxide dismutase and catalase) and increased ascorbic acid content; (iv) ameliorated microbial spoilage by inhibiting bacterial growth, especially Serratia, a major bacterial community on the surface of F. velutipes; (v) enhanced chitin content and thereby maintained structural integrity; and (vi) maintained levels of Asp, Glu, linoleic acid, and polyunsaturated fatty acids. In conclusion, IAITC reduced catalase activity and total phenolic content in F. velutipes during storage. The most suitable concentration of IAITC in the preservation of F. velutipes was 50 µL L−1.