The advancement of low-altitude intelligent networks enables unmanned aerial vehicle (UAV) interconnection via flying ad-hoc networks (FANETs), offering flexibility and decentralized coordination. However, resource constraints, dynamic topologies, and UAV operations in open environments present significant security and communication challenges. Existing multi-factor and public-key cryptography protocols are vulnerable due to their reliance on stored sensitive information, increasing the risk of exposure and compromise. This paper proposes a lightweight authentication and key agreement protocol for FANETs, integrating physical unclonable functions with dynamic credential management and lightweight cryptographic primitives. The protocol reduces computational and communication overhead while enhancing security. Security analysis confirms its resilience against various attacks, and comparative evaluations demonstrate its superiority in security, communication efficiency, and computational cost.