Unmanned aerial vehicles (UAVs) play a critical role in various fields, including logistics, agriculture, and rescue operations. Effective identity authentication and key agreement schemes are vital for UAV networks to combat threats. Current schemes often employ algorithms like elliptic curve cryptography (ECC) and Rivest–Shamir–Adleman (RSA), which are vulnerable to quantum attacks. To address this issue, we propose LIGKYX, a novel scheme combining the quantum-resistant Kyber algorithm with the hash-based message authentication code (HMAC) for enhanced security and efficiency. This scheme enables the mutual authentication between UAVs and ground stations and supports secure session key establishment protocols. Additionally, it facilitates robust authentication and key agreement among UAVs through control stations, addressing the critical challenge of quantum-resistant security in UAV networks. The proposed LIGKYX scheme operates based on the Kyber algorithm and elliptic curve Diffie–Hellman (ECDH) key exchange protocol, employing the HMAC and pre-computation techniques. Furthermore, a formal verification tool validated the security of LIGKYX under the Dolev–Yao threat model. Comparative analyses on security properties, communication overhead, and computational overhead indicate that LIGKYX not only matches or exceeds existing schemes but also uniquely counters quantum attacks effectively, ensuring the security of UAV communication networks with a lower time overhead for authentication and communication.