The invention puts forward a USB (Universal Serial Bus) flash disk secure storage method based on the virtual file system, which constructs a virtual disk in a USB flash disk on the basis of the virtual file system and adopts a multi-level security measure to protect data, so that the storage and use of the USB flash disk are safer and more reliable. The technical scheme is as follows: a secure partition is allocated in the USB flash disk and formatted into the virtual file system as a virtual disk which exists in the form of a file but actually is a file system; on the basis of the unique identifier of the USB flash disk, the USB flash disk is bounded with the virtual disk to prevent copy; entering the virtual disk requires a user to input a key, and the key inputted by the user is protected by a specific generating algorithm and a key management mechanism; the virtual disk is encrypted and decrypted; the user also can bind a computer using the virtual disk in order to control access to the virtual disk.