The present invention discloses a content protection system in a storage medium and the method of the same. The storage medium includes a flash disk, a memory card, a hard disk, a CDR, or a MO. In one aspect of the present invention, the content protection system in a storage medium includes a database; a partitioning module coupled to the database to partition the storage medium; and a link table managing module coupled to the database to establish and manage a link table of a file to be stored in the storage medium.