Due to possible disturbances in a conflict environment, the mission performance of flying ad hoc networks (FANET) is highly related to time-varying topology. Currently, the resilience metric is regarded as suitable for evaluating the mission performance of a FANET with time-varying network topology. However, the reported resilience studies contribute little to the theoretical analysis of the impact of the time-varying topology of FANET on a cooperative mission. In this article, an improved resilience analysis method is proposed by defining a new dimension reduction operator, which takes into account the impacts of both isolated and communicated unmanned aerial vehicles. Then, based on random geometry theory, the topological features of FANET are extracted to measure the structure perturbation and recovery. A case study of a joint reconnaissance mission shows that our analysis method is more realistic than the typical method. Our results may be helpful to analyze the resilience of networked dynamic systems and support the more flexible topology control methods design of a FANET.