Existing fault diagnosis methods usually assume that there are balanced training data for every machine health state. However, the collection of fault signals is very difficult and expensive, resulting in the problem of imbalanced training dataset. It will degrade the performance of fault diagnosis methods significantly. To address this problem, an imbalanced fault diagnosis of rotating machinery using autoencoder-based SuperGraph feature learning is proposed in this paper. Unsupervised autoencoder is firstly used to compress every monitoring signal into a low-dimensional vector as the node attribute in the SuperGraph. And the edge connections in the graph depend on the relationship between signals. On the basis, graph convolution is performed on the constructed SuperGraph to achieve imbalanced training dataset fault diagnosis for rotating machinery. Comprehensive experiments are conducted on a benchmarking publicized dataset and a practical experimental platform, and the results show that the proposed method can effectively achieve rotating machinery fault diagnosis towards imbalanced training dataset through graph feature learning.