The present invention discloses a method of controlling a robot system and an apparatus thereof. The method of controlling a robot system in accordance with an embodiment of the present invention can include: initializing the master controller by use of a boot loader equipped in the robot system; executing a runtime by loading a runtime execution code stored in a storage space of the master controller; and loading and executing an application program stored in the storage space of the master controller. With an embodiment of the present invention, it becomes possible to manage the application program more efficiently for realizing the functions of the robot system.