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The integration of heterogeneous aviation information networks (HAIN) has recently attracted significant attention among researchers. An important topic requiring discussion is the method by which timely and accurate information may be acquired to ensure aviation safety and facilitate risk evaluation. This paper proposes a distributed gateway clustering framework, whereby gateways collaborate and cooperate with each other to achieve load balancing and cooperative communication for the integration of HAIN. Unlike traditional approaches, in the framework, a cooperative architecture is presented for HAIN interoperability and load preference is taken into account to cater to the specialized nature of HAIN through describing load matrix. Two approaches are proposed for load allocation: 1) the load preference allocation (LPA) algorithm at the subnet level in which each subnet is controlled by the same gateway with predictive load assignment by incorporating the historical load information of each subnet; and 2) the gateway cooperative load allocation (GCLA) algorithm at the gateway level aimed to balance the distribution of traffic load among gateways globally. The related parameters of operating efficiency and processing time are used to analyze and evaluate the performance of the proposed load allocation algorithms of the integrated HAIN system. Simulation results are presented to show the effectiveness of the proposed framework.