Data-driven fault diagnosis techniques are frequently applied to ensure the reliability and safety of industrial systems. However, as a common challenge, the class-imbalance problem reduces the performance of data-driven methods due to the lack of data information. We propose a weighted modified conditional variational auto-encoder (WM-CVAE) as a novel data augmentation technique to tackle the issue. The modified structure can alleviate the existing Kullback–Leibler (KL) divergence vanishing by an adaptive loss. Meanwhile, kernel mean matching (KMM) is proposed on weight computation to reduce the negative effect of dissimilar generated samples. Constructing the WM-CVAE data augmentation framework can effectively improve the data quality and learning capability in class-imbalance fault diagnosis. To validate the proposed WM-CVAE model, three real-world industrial datasets are used as study objects, and the random forest is used as the base learner in the fault classification tasks. The diagnostic results demonstrate that the proposed WM-CVAE data augmentation framework can improve learning results in class-imbalance fault diagnosis.