As Flying Ad-hoc Network (FANET) evolves toward larger scales and higher levels of autonomy, the importance of secure and efficient group communication continues to grow. However, resource-constrained unmanned aerial vehicles (UAVs) face dual challenges: limited computational power struggles to meet the high demands of complex cryptographic algorithms, while bandwidth constraints exacerbate communication overhead caused by multi-round interaction mechanisms. Moreover, existing solutions find it hard to support dynamic group environments and are prone to single point of failure (SPoF) in centralized architectures, which significantly compromises system reliability and scalability. To address these issues, this paper proposes a novel key agreement protocol for FANET. The protocol employs an improved tree-based key encapsulation mechanism (iTreeKEM) to support rapid key updates in highly dynamic environments. It reduces the computational cost for each group member by 90.08% even when the group size reaches 128. To further enhance system robustness, the protocol introduces a smart contract-based distributed leader election mechanism, effectively eliminating SPoF. The security of the proposed protocol is guaranteed by the CDH problem under the generalized selective decryption (GSD) model. Finally, we implement the protocol in NS-3 simulations, and the results demonstrate its effective applicability to FANET.