In order to solve the multiple uncertain problems such as the operation sequence and operation time of the carrier-based aircraft on the ship’s support, a fast flight scheduling algorithm for carrier-borne aircraft is designed. Aircraft deck to ensure job combination optimization scheduling model is established, the encoding mode of algorithm structure is introduced, the appropriate strategy of genetic algorithm is used to calculate and effective scheduling scheme is given. Based on the basic static scheduling scheme, the current effective fast scheduling schemes is acquired by using dynamic scheduling adjustment, and the effectiveness of the algorithm is validated by simulation examples. The simulation results show that the optimal scheduling scheme can be obtained by using this algorithm.