The invention provides a numerical control system authority management method based on the USB flash disk physical serial number. The method comprises the steps that an authority management module extracts the physical serial number of a USB flash disk connected with the authority management module according to the Windows interface function; the authority management module decodes an encrypted authorized file stored in the USB flash disk, and checks whether a verifying physical sequence number in the encrypted authorized file is consistent with the physical serial number of the USB flash disk or not; if yes, management over a numerical control system is authorized, and if not, management over the numerical control system is not authorized, wherein the encrypted authorized file comprises the verifying physical serial number, user identification, unit identification, the authorization time limit and the authorization rank. As the general USB flash disk is used, no additional hardware cost is increased, and the defect of an existing numerical control system authority management method can be effectively improved.