The continuous growth of air traffic has led to acute airspace congestion and severe delays, which threatens operation safety and cause enormous economic loss. Flight assignment is an economical and effective strategic plan to reduce the flight delay and airspace congestion by reasonably regulating the air traffic flow of China. However, it is a large-scale combinatorial optimization problem which is difficult to solve. In order to improve the quality of solutions, an effective multi-objective parallel evolution algorithm (MPEA) framework with dynamic migration interval strategy is presented in this work. Firstly, multiple evolution populations are constructed to solve the problem simultaneously to enhance the optimization capability. Then a new strategy is proposed to dynamically change the migration interval among different evolution populations to improve the efficiency of the cooperation of populations. Finally, the cooperative co-evolution (CC) algorithm combined with non-dominated sorting genetic algorithm II (NSGA-II) is introduced for each population. Empirical studies using the real air traffic data of the Chinese air route network and daily flight plans show that our method outperforms the existing approaches, multi-objective genetic algorithm (MOGA), multi-objective evolutionary algorithm based on decomposition (MOEA/D), CC-based multi-objective algorithm (CCMA) as well as other two MPEAs with different migration interval strategies.