A method and apparatus for transmitting, receiving, and storing files based on a predetermined container structure are provided. The method includes identifying some or all of files to be transmitted among the stored files; generating transmission information for the identified files and transmitting the transmission information to the receiving device; configuring a header including information about the location of the directory in which each of the identified files is to be stored; and adding the configured header to each of the identified files and transmitting the header-added files to the receiving device.