The civil aircraft flight deck door system is installed in the aircraft cabin to block the cockpit area and cabin area. In addition to providing normal access to the cockpit, it must have bullet proof and intrusion prevention functions to prevent non-crew members from seizing control of the aircraft and provide safety protection for crew members. This paper starts with the interpretation of the airworthiness provisions for the flight deck door system to resist penetration, studies and interprets the airworthiness certification requirements, raises a evaluation method of civil aircraft flight deck door to resist penetration, gives the test implementation details and requirements such as bullet selection, dangerous trajectory confirmation, shooting point screening, test piece configuration preparation, and verifies it based on the development of a civil aircraft flight deck door system and the airworthiness certification for resisting penetration, The results show that the method is effective and can show the compliance of the clauses. The research content of this paper can provide reference for aircraft flight deck door design and development, airworthiness compliance analysis and verification, and airworthiness certification of relevant clauses.