An auto-synchronization method, apparatus, and system for synchronizing compressed content file automatically in such a way of tracing the modification history of source files of the compressed content file and synchronizing the modified source files selectively are provided. The portable device includes a radio communication unit configured to connect to the synchronization server to transmit and receive data related to the compressed content file, a storage unit configured to store at least one of the compressed content file, compressed content file information, and source file information related to source files constituting the compressed content file, and a control unit configured to detect a synchronization request signal generated by an event modifying the compressed content file, extract at least one modified first source file from the compressed content file based on the source file information, and synchronize the extracted first source file with a second source file matching among source files stored in a synchronization server.