In view of the characteristics of airborne networks, such as the traffic data of 1553B data bus and public networks, numerous redundant and irrelevant data, and fewer but more types of attack behaviors, a highly representative balanced data subset is generated by combining K-means with synthetic minority oversampling technique (SMOTE). A feature selection (FS) method of fast correlation-based filter combined with information gain (IG-FCBF) is proposed to filter the key characteristics with 90 % cumulative importance. Aiming at the problem that it is not easy for a single classifier to accurately classify various types of attacks, as well as the difficulty in obtaining the best prediction results by adjusting default and manual parameters, a multi-layer ensemble model based on Bayesian optimization tree-structured Parzen estimator (BO-TPE) is proposed for airborne networks intrusion detection, combining the advantages of supervised learning, stacking ensemble method and hyperparameter optimization (HPO). The experimental results show the superiority and effectiveness of the model, as well as its universality in Integrated Avionics Systems (IAS) and onboard public networks, which provides a new approach for airborne networks intrusion identification and protection.