A forged command filtering system includes: a secure command generating device for performing a digital signature operation on a selected command to generate a command request; a command transmitting device for receiving and transmitting the command request; a target device; and a command authentication circuit. The command authentication circuit includes: a communication interface for communicating with the command transmitting device or the target device; a secure micro-controller for storing a signature verification key of the secure command generating device; a control circuit for cooperating with the secure micro-controller to authenticate the command request using the signature verification key; and a storage circuit for storing data required for the operations of the control circuit. The control circuit further instructs the target device to execute a target command corresponding to the command request only if the command request passed the authentication processes of the secure micro-controller and the control circuit.