To analyze a collection of interconnected documents, relational topic models (RTMs) have been developed to describe both the link structure and document content, exploring their underlying relationships via a single-layer latent representation with limited expressive capability. To better utilize the document network, we first propose graph Poisson factor analysis (GPFA) that constructs a probabilistic model for interconnected documents and also provides closed-form Gibbs sampling update equations, moving beyond sophisticated approximate assumptions of existing RTMs. Extending GPFA, we develop a novel hierarchical RTM named graph Poisson gamma belief network (GPGBN), and further introduce two different Weibull distribution based variational graph auto-encoders for efficient model inference and effective network information aggregation. Experimental results demonstrate that our models extract high-quality hierarchical latent document representations, leading to improved performance over baselines on various graph analytic tasks.