This paper studies the fundamental problem of multi-layer generator models in learning hierarchical representations. The multi-layer generator model that consists of multiple layers of latent variables organized in a top-down architecture tends to learn multiple levels of data abstraction. However, such multi-layer latent variables are typically parameterized to be Gaussian, which can be less informative in capturing complex abstractions, resulting in limited success in hierarchical representation learning. On the other hand, the energy-based (EBM) prior is known to be expressive in capturing the data regularities, but it often lacks the hierarchical structure to capture different levels of hierarchical representations. In this paper, we propose a joint latent space EBM prior model with multi-layer latent variables for effective hierarchical representation learning. We develop a variational joint learning scheme that seamlessly integrates an inference model for efficient inference. Our experiments demonstrate that the proposed joint EBM prior is effective and expressive in capturing hierarchical representations and modelling data distribution.