Nowadays, unmanned aerial vehicles (UAVs) are used in various fields due to their high maneuverability and low cost of construction and use. With the development of UAV technology, it has become a trend for UAVs to cooperate with each other to complete assigned tasks. Multiple UAVs are combined according to a certain structure, and through the information sharing between them, a cooperative effect is generated to achieve intelligent collaborative task execution. However, information sharing is carried out on a public channel, so ensuring secure communication between UAVs is crucial. Moreover, UAVs are easily captured by an adversary, who can impersonate legitimate UAVs to disrupt communications if UAVs’ internal secrets that are stolen. Therefore, we propose a lightweight authentication scheme based on physical unclonable function (PUF), to provide mutual authentication between UAVs. PUF is embedded in the unmanned aerial vehicle (UAV) to defend against physical capture attack. Furthermore, to evaluate the security and performance of our scheme, formal and informal security analyses and formal security verification of the scheme are performed, and the performance of the scheme is compared with existing UAV schemes. The above analyses show that our scheme has great advantages in terms of security and overheads.