The efficient scheduling of carrier aircraft support operations in the flight deck is important for battle performances. The supporting operations and maintenance processes involve multiple support resources, complex scheduling process, and multiple constraints; the efficient coordination of these processes can be considered a multi-resource constrained multi-project scheduling problem (MRCMPSP), which is a complex non-deterministic polynomial-time hard (NP-hard) problem. The renewable resources include the operational crews, resource stations, and operational spaces, and the non-renewable resources include oil, gas, weapons, and electric power. An integer programming mathematical model is established to solve this problem. A periodic and event-driven rolling horizon (RH) scheduling strategy inspired by the RH optimization method from predictive control technology is presented for the dynamic scheduling environment. The periodic horizon scheduling strategy can track the changes of the carrier aircraft supporting system, and the improved event-driven mechanism can avoid unnecessary scheduling with effective resource allocation under uncertain conditions. The dual population genetic algorithm (DPGA) is designed to solve the large-scale scheduling problem. The activity list encoding method is proposed, and a new adaptive crossover and mutation strategy is designed to improve the global exploration ability. The double schedule for leftward and rightward populations is integrated into the genetic process of alternating iterations to improve the convergence speed and decrease the computation amount. The computational results show that our approach is effective at solving the scheduling problem in the dynamic environment, as well as making better decisions regarding disruption on a real-time basis.