Domain adaptation (DA) is an effective solution for addressing the domain shift problem. However, existing DA techniques usually directly match the distributions of the data in the original feature space, where some of the features may be distorted by a large domain shift. Besides, geometric and clustering structures of the data, which play a significant role in revealing hidden failure patterns, are not considered in traditional DA methods. To tackle the above issues, a new joint soft clustering and distribution alignment with graph embedding (JSCDA-GE) method is proposed. Specifically, weighted subspace alignment (WSA) is proposed to align bases of source and target subspaces by combining instance reweighting and subspace alignment strategies. Then, JSCDA-GE formulates an objective function by incorporating dynamic distribution alignment (DDA), soft large margin clustering (SLMC), and graph embedding (GE) in a unified structural risk minimization (SRM) framework. Ultimately, JSCDA-GE aims to learn a generalization classifier for fault diagnosis. Its effectiveness and superiority have been confirmed through thirty-six tasks on two bearing databases.