We consider the semi-supervised clustering problem where crowdsourcing provides noisy information about the pairwise comparisons on a small subset of data, i.e., whether a sample pair is in the same cluster. We propose a new approach that includes a deep generative model (DGM) to characterize low-level features of the data, and a statistical relational model for noisy pairwise annotations on its subset. The two parts share the latent variables. To make the model automatically trade-off between its complexity and fitting data, we also develop its fully Bayesian variant. The challenge of inference is addressed by fast (natural-gradient) stochastic variational inference algorithms, where we effectively combine variational message passing for the relational part and amortized learning of the DGM under a unified framework. Empirical results on synthetic and real-world datasets show that our model outperforms previous crowdsourced clustering methods.