Open-set Classification (OSC) is a critical requirement for safely deploying machine learning models in the open world, which aims to classify samples from known classes and reject samples from out-of-distribution (OOD). Existing methods exploit the feature space of trained network and attempt at estimating the uncertainty in the predictions.However, softmax-based neural networks are found to be overly confident in their predictions even on data they have never seen before andthe immense diversity of the OOD examples also makes such methods fragile.To this end, we follow the idea of estimating the underlying density of the training data to decide whether a given input is close to the in-distribution (IND) data and adopt Energy-based models (EBMs) as density estimators. A novel energy-based generative open-set node classification method, \textit{EGonc}, is proposed to achieve open-set graph learning. Specifically, we generate substitute unknowns to mimic the distribution of real open-set samples firstly, based on the information of graph structures. Then, an additional energy logit representing the virtual OOD class is learned from the residual of the feature against the principal space, and matched with the original logits by a constant scaling. This virtual logit serves as the indicator of OOD-ness. EGonc has nice theoretical properties that guarantee an overall distinguishable margin between the detection scores for IND and OOD samples. Comprehensive experimental evaluations of EGonc also demonstrate its superiority.