Early detection of faults is of importance to avoid catastrophic accidents and ensure safe operation of machinery. A novel graph neural network-based fault detection method is proposed to build a bridge between AI and real-world running mechanical systems. First, the vibration signals, which are Euclidean structured data, are converted into graph (non-Euclidean structured data), so that the vibration signals, which are originally independent of each other, are correlated with each other. Second, inputs the dataset together with its corresponding graph into the GNN for training, which contains graphs in each hidden layer of the network, enabling the graph neural network to learn the feature values of itself and its neighbors, and the obtained early features have stronger discriminability. Finally, determines the top-n objects that are difficult to reconstruct in the output layer of the GNN as fault objects. A public datasets of bearings have been used to verify the effectiveness of the proposed method. We find that the proposed method can successfully detect faulty objects that are mixed in the normal object region.