The invention discloses file executing method and system and a programmable storage device, which is used for executing computer execution code groups stored in a hidden storage area of the storage device in a working system of a computer host. The method comprises the following steps of: connecting the storage device to the computer host and providing a loading program to manage the computer execution code groups stored in the hidden storage area. The method further comprises the following steps of: running the loading program in a main memory of the computer host; requesting the working system to distribute a first address section for running the loading program in the main memory; loading the computer execution code groups from the hidden storage area into the first address section by the loading program; converting the loaded computer execution code groups into executable content capable of being executed by the working system and storing the converted executable content into the first address section by the loading program; and executing a derivational executing program to execute the converted executable content by the loading program.