Present invention provides a method and an apparatus for deleting duplicate data. The method include: receiving a modified data block for a user file stored in the data storage system; querying whether the modified data block is found in the system data block file; if the modified data block is not found in the system data block file, adding the modified data block to the system data block file, and updating an index relationship of the user file with the system data block file to include an index pointing to the modified data block added in the system data block file. With the method and apparatus for deleting duplicate data provided by embodiments of the present invention, the duplicate data after modification is deleted, which improves the performance in modifying other data block files and improves the effect of deleting the duplicate data.