We propose a new algorithmic framework for learning autoencoders of data distributions. In this framework, we minimize the discrepancy between the model distribution and the target one, with relational regularization on learnable latent prior. This regularization penalizes the fused Gromov-Wasserstein (FGW) distance between the latent prior and its corresponding posterior, which allows us to learn a structured prior distribution associated with the generative model in a flexible way. Moreover, it helps us co-train multiple autoencoders even if they are with heterogeneous architectures and incomparable latent spaces. We implement the framework with two scalable algorithms, making it applicable for both probabilistic and deterministic autoencoders. Our relational regularized autoencoder (RAE) outperforms existing methods, e.g., variational autoencoder, Wasserstein autoencoder, and their variants, on generating images. Additionally, our relational co-training strategy of autoencoders achieves encouraging results in both synthesis and real-world multi-view learning tasks.