Convolutional autoencoders (CAEs) have shown their remarkable performance in stacking to deep convolutional neural networks (CNNs) for classifying image data during the past several years. However, they are unable to construct the state-of-the-art CNNs due to their intrinsic architectures. In this regard, we propose a flexible CAE (FCAE) by eliminating the constraints on the numbers of convolutional layers and pooling layers from the traditional CAE. We also design an architecture discovery method by exploiting particle swarm optimization, which is capable of automatically searching for the optimal architectures of the proposed FCAE with much less computational resource and without any manual intervention. We test the proposed approach on four extensively used image classification data sets. Experimental results show that our proposed approach in this paper significantly outperforms the peer competitors including the state-of-the-art algorithms.