Performing clustering analysis on a large amount of historical trajectory data can obtain information such as frequent flight patterns of aircraft and air traffic flow distribution, which can provide a reference for the revision of standard flight procedures and the optimization of the division of airspace sectors. At present, most trajectory clustering uses a single clustering algorithm. When other processing remains unchanged, it is difficult to improve the clustering effect by using a single clustering method. Therefore, this paper proposes a trajectory clustering ensemble method based on a similarity matrix. Firstly, a stacked autoencoder is used to learn a small number of features that are sufficiently representative of the trajectory and used as the input to the subsequent clustering algorithm. Secondly, each basis cluster is used to cluster the data set, and then a consistent similarity matrix is obtained by using the clustering results of each basis cluster. On this basis, using the deformation of the matrix as the distance matrix between trajectories, the agglomerative hierarchical clustering algorithm is used to ensemble the results of each basis cluster. Taking the Nanjing Lukou Airport terminal area as an example, the experimental results show that integrating multiple basis clusters eliminates the inherent randomness of a single clustering algorithm, and the trajectory clustering results are more robust.