The invention provides a method for processing an illegal optical network unit (ONU) by a GPON system, comprising the following steps: firstly, the ONU reports an equipment serial number of the ONU toan OLT; secondly, a detecting device detects the received equipment serial number, if the equipment serial number is illegal, the detecting device records the equipment serial number, and the OLT sends a message of entering into an emergency stopping state to the ONU. The invention makes up the blank of a GPON protocol, provides a method for reasonably processing the illegal ONU under the condition that the equipment serial number of the ONU does not pass the authentification and provides the condition of the action and the state of the ONU.