3D data that contains rich geometry information of objects and scenes is valuable for understanding 3D physical world. With the recent emergence of large-scale 3D datasets, it becomes increasingly crucial to have a powerful 3D generative model for 3D shape synthesis and analysis. This paper proposes a deep 3D energy-based model to represent volumetric shapes. The maximum likelihood training of the model follows an analysis by synthesis scheme. The benefits of the proposed model are six-fold: first, unlike GANs and VAEs, the model training does not rely on any auxiliary models; second, the model can synthesize realistic 3D shapes by Markov chain Monte Carlo (MCMC); third, the conditional model can be applied to 3D object recovery and super resolution; fourth, the model can serve as a building block in a multi-grid modeling and sampling framework for high resolution 3D shape synthesis; fifth, the model can be used to train a 3D generator via MCMC teaching; sixth, the unsupervisedly trained model provides a powerful feature extractor for 3D data, which is useful for 3D object classification. Experiments demonstrate that the proposed model can generate high-quality 3D shape patterns and can be useful for a wide variety of 3D shape analysis.