This invention discloses a control system and method thereof that is applied to a navigation apparatus. The system includes an apparatus body, a tag, a reader, a recognition module, and a processor. The apparatus body is mounted in the navigation apparatus to provide a navigation function. The tag is mounted on an object to provide a recognition data. The reader is used to detect and read the recognition data. The recognition module is used to compare the recognition data with a predetermined recognition data in order to generate a trigger signal. The processor is used to receive the trigger signal and then drives the apparatus body to perform a wakeup mode. If the processor does not receive the trigger signal in a determined period, the processor will drive the apparatus body to perform a sleep mode.