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Since industrial process data often presents strong correlations, high complexity, and nonlinear patterns, a proficient deep learning model is required for the fault classification task. Recent researches have shown that deep learning models like stacked autoencoder (SAE) are able to learn deep abstract features from complex process data. Nevertheless, a traditional SAE cannot extract the informative fault-relevant features and data distribution features from industrial process data, which are necessary for effective fault classification in industrial processes. Thus, this study proposes a semi-supervised Inter-Relational Mahalanobis SAE (IRM-SAE) model to learn inter-relational distribution and fault-relevant dynamic features of process data for fault classification. First, the Inter-Relational Mahalanobis loss is introduced into the original objective function of SAE to learn meaningful inter-relational distribution features within the data. Then, an active time frame technique is developed to preprocess the input data to capture the dynamic features of the data. Furthermore, to fully utilize both labeled and unlabeled data in industrial processes, the semi-supervised strategy is introduced to learn fault-related features for better fault classification. To validate the performance of the proposed model, it is applied on the Tennessee–Eastman process and a real-world industrial hydrocracking process. The experimental results show that the proposed model has higher fault classification performance compared to other deep learning models. • A novel semi-supervised Inter-Relational Mahalanobis SAE (IRM-SAE) model is proposed to learn inter-relational distribution and fault-relevant dynamic features of process data. • An active time frame technique is developed to preprocess the process data to capture the dynamic features of the data. • To fully utilize both labeled and unlabeled data in industrial processes, the semi-supervised strategy is introduced to learn fault-related features for better fault classification. • The experimental results on two industrial processes show that the proposed model has higher fault classification performance compared to other deep learning models. [ABSTRACT FROM AUTHOR]