Traditional intelligent fault diagnosis methods focus on distinguishing different fault modes, but ignore the deterioration of fault severity. This paper proposes a new two-stage hierarchical convolutional neural network for fault diagnosis of rotating machinery bearings. The failure mode and failure severity are modeled as a hierarchical structure. First, the original vibration signal is transformed into an energy spectrum matrix containing fault-related information through wavelet packet decomposition. Secondly, in the model training method, an adaptive learning rate dynamic adjustment strategy is further proposed, which adaptively extracts robust features from the spectrum matrix for fault mode and severity diagnosis. To verify the effectiveness of the method, the bearing fault data was collected using a rotating machine test bench. On this basis, the diagnostic accuracy, convergence performance and robustness of the model under different signal-to-noise ratios and variable load environments are evaluated, and the feature learning ability of the method is verified by visual analysis. Experimental results show that this method has achieved satisfactory results in both fault pattern recognition and fault severity evaluation, and is superior to other machine learning and deep learning methods.