In this paper, a quantum identity authentication protocol is presented based on the counterfactual quantum key distribution system. Utilizing the proposed protocol, two participants can verify each other’s identity through the counterfactual quantum communication system. The security of the protocol is proved against individual attacks. Furthermore, according to the characteristics of the counterfactual quantum key distribution system, we propose an authenticated counterfactual quantum key distribution protocol based on a novel strategy of mixing the two types of quantum cryptographic protocols randomly. The authenticated quantum key distribution can also be used to update the extent of the authentication keys.