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Air traffic delay is a critical and expensive problem for multi-airport systems. One strategy for reducing total delay cost is to optimize the flight schedule. The SIMMOD software developed by FAA can be used to build simulation model for the multi-airport system. Based on the restricted SPSA optimization algorithm and the theory of multi-level programming model, an area multi-airport system simulation optimization model and algorithm was proposed. This model and algorithm take the importance of related route network nodes and the expected value of optimization results into account. The simulation optimization results of the PRD region multi-airport system verified the effectiveness of the model and algorithm.