A method and apparatus controls an MTP device to manage a media file transmitted by an MTP host. According to the method, when the number of files in a folder assigned by the MTP host is equal to or more than a predetermined number while storing a media file received from the MTP host, the MTP device generates a new folder and stores the corresponding media file in the new folder. Accordingly, the files within the predetermined number can be stored in one file. Since the number of files stored in one folder is limited, delay in processing media files due to the large number of files can be reduced.