A data updating system, an embedded electronic device and a data updating method are provided. The data updating system includes the embedded electronic device and an auxiliary updating device. The embedded electronic device has a serial transmission port. The auxiliary updating device is coupled to the serial transmission port of the embedded electronic device. The embedded electronic device in a normal mode transmits a periodic signal to the auxiliary updating device through the serial transmission port, and the auxiliary updating device transmits status information to the embedded electronic device according to the periodic signal. If the status information is mode switching information, the embedded electronic device enters a special mode, and the embedded electronic device in the special mode receives update data from the auxiliary updating device through the serial transmission port to update internal data of the embedded electronic device.