The present invention provides a debugging system and method for an embedded device, including: an embedded device, including a processing unit and a memory unit, where the memory unit includes a staging area used to store debugging data; a mobile storage device, including a debugging data control unit and a storage unit; and a computer, electrically connected to the embedded device and the mobile storage device. The debugging data control unit transmits a debugging demand message to the embedded device by using the computer. The embedded device transmits the debugging data in the staging area back to the computer. The computer transmits the debugging data to the mobile storage device and stores the debugging data in the storage unit.