Data-driven techniques improve the quality of talent training comprehensively for university by discovering potential academic problems and proposing solutions. We propose an interpretable prediction method for university student academic crisis warning, which consists of K-prototype-based student portrait construction and Catboost–SHAP-based academic achievement prediction. The academic crisis warning experiment is carried out on desensitization multi-source student data of a university. The experimental results show that the proposed method has significant advantages over common machine learning algorithms. In terms of achievement prediction, mean square error (MSE) reaches 24.976, mean absolute error (MAE) reaches 3.551, coefficient of determination ($$R^{2}$$
R
2
) reaches 80.3%. The student portrait and Catboost–SHAP method are used for visual analysis of the academic achievement factors, which provide intuitive decision support and guidance assistance for education administrators.
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