The invention discloses a master-slave interchangeable double-redundancy control device based on a distributed system and a method thereof, wherein the control device is used for an underwater glider.According to the device, a distributed CAN bus is used as a hardware architecture; devices such as a double-CPU common storage area, a power supply mutual control device and a double-switch signal triggering device are respectively established. According to the method, through hardware designing, a foundation of a master-slave interchangeable control right is established, and then CPU crash statemutual determining is performed through a continuous pulse hardware scanning method. Then an appropriate hardware restarting operation is performed. According to the master-slave interchangeable double-redundancy control device, the master-slave interchangeable CPU is used for preventing a condition of single central controller problem in a designing method of stripping a master control right, thereby improving system reliability.