Multiple unmanned aerial vehicle (multi-UAV) system is a type of dynamic spatiotemporal Internet of Things and susceptible to destruction from the external environment. Meanwhile, resilience theory has been introduced to describe the ability of unmanned aerial vehicles (UAVs) faced with disturbances. However, the existing methods do not fully reflect the dynamic spatiotemporal characteristics of multi-UAV systems. Therefore, we proposed a novel resilience metric that integrates mission coverage area and communication status to describe the dynamic spatiotemporal characteristics of multi-UAV systems. On the basis, a combination of importance measures for vulnerability, recoverability, and resilience is presented to support the analysis and identification of weaknesses for the system in whole process. Furthermore, a structure design method is given to improve system resilience by considering both importance measures and trajectory optimization methods simultaneously. Finally, a typical formation topology with six UAVs is simulated as a case study to verify the proposed approach.