In complex industrial environments, the vibration signal of the rolling bearing is covered by noise, which makes fault diagnosis inaccurate. In order to overcome the effect of noise on the signal, a rolling bearing fault diagnosis method based on the WOA-VMD (Whale Optimization Algorithm-Variational Mode Decomposition) and the GAT (Graph Attention network) is proposed to deal with end effect and mode mixing issues in signal decomposition. Firstly, the WOA is used to adaptively determine the penalty factor and decomposition layers in the VMD algorithm. Meanwhile, the optimal combination is determined and input into the VMD, which is used to decompose the original signal. Then, the Pearson correlation coefficient method is used to select IMF (Intrinsic Mode Function) components that have a high correlation with the original signal, and selected IMF components are reconstructed to remove the noise in the original signal. Finally, the KNN (K-Nearest Neighbor) method is used to construct the graph structure data. The multi-headed attention mechanism is used to construct the fault diagnosis model of the GAT rolling bearing in order to classify the signal. The results show an obvious noise reduction effect in the high-frequency part of the signal after the application of the proposed method, where a large amount of noise was removed. In the diagnosis of rolling bearing faults, the accuracy of the test set diagnosis in this study was 100%, which is higher than that of the four other compared methods, and the diagnosis accuracy rate of various faults reached 100%.