Distributed flying ad hoc networks (FANETs) have been widely used in collaborative reconnaissance, situation construction, and other scenarios. In distributed FANETs with multi-hop and intermittent links, nodes only maintain neighbors' information and cannot obtain knowledge of the whole network. There may be contradicting information collected across nodes, resulting in inconsistency problems. However, existing research on collaborative consensus focuses mainly on the control domain using multi-agent consensus theory. The study on distributed network consensus does not consider the effect of the multi-hop forwarding sequence, hence limiting distributed FANETs optimization. Based on this, we establish a network consensus model utilizing the multi-agent consensus theory and analyze the impact of outage probability of links and untimely forwarding on the distributed consensus probability, considering the node density, link outage probability, and network maintenance times. Besides, using the election mechanism as an example, we establish distributed network performance analysis models considering consensus error to enhance the performance analysis of service delay and resource efficiency of distributed FANETs. Finally, we construct a protocol-level simulation platform based on Visual Studio and extensive experiments to validate the model’s accuracy and figure out the optimal mechanism parameters under different network and channel parameters. The simulation results show that the optimal network maintenance times increase with the increasing outage probability of links. Moreover, distributed FANETs can achieve optimal resource efficiency without achieving complete consensus; that is, there is a tradeoff between network maintenance cost and network consensus performance.