Vibration signals always contain noise and irregularities, which makes spectrum analysis difficult to extract high-level features. Recently, graph theory has been applied to spectrum analysis to improve the performance of feature extraction. By converting the raw data into graphs, hidden structural and topological information can be obtained. In this article, a spatial-temporal graph-based feature extraction, called SuperGraph, for rotating machinery fault diagnosis is proposed. Specifically, graph theory-based spectrum analysis is used to construct the spatial-temporal graph. Then, the Laplacian matrix-based feature vector is extracted from the constructed spatial-temporal graph. By this means, the spatial-temporal graph is converted into the one-dimensional (1-D) vector for further constructing SuperGraph, where each node of the SuperGraph represents a spatial-temporal graph and the SuperGraph is composed of many local graphs. In the local graph, only the same type of nodes are connected to form a fully connected graph. Thus, the task of graph classification can be transformed into classifying the nodes in the SuperGraph. After graph convolutional network is established for learning and obtaining deep features, the label of nodes is identified from a <inline-formula><tex-math notation="LaTeX">$softmax$</tex-math></inline-formula> model. Experiments are conducted on two benchmarking datasets and a practical experimental platform to verify effectiveness of the proposed fault diagnosis method.