A method of managing data of a file system includes: obtaining information of an unallocated inode that is not currently used because a corresponding file has been deleted based on status of use of inodes stored in an inode bitmap and deletion information of the inodes stored in an inode table; retrieving a backup inode corresponding to the unallocated inode in a journal log area using the obtained information of the unallocated inode; and requesting selection of whether to permanently delete files corresponding to the retrieved backup inode.