Intelligent learning diagnosis is a critical engine of intelligent tutoring systems, which aims to estimate learners’ current knowledge mastery status and predict their future learning performance. The significant challenge with traditional learning diagnosis methods is the inability to balance diagnostic accuracy and interpretability. Although the existing psychometric-based learning diagnosis methods provide some domain interpretation through cognitive parameters, they have insufficient modeling capability with a shallow structure for large-scale learning data. While the deep learning-based learning diagnosis methods have improved the accuracy of learning performance prediction, their inherent black-box properties lead to a lack of interpretability, making their results untrustworthy for educational applications. To settle the abovementioned problem, the proposed unified interpretable intelligent learning diagnosis framework, which benefits from the powerful representation learning ability of deep learning and the interpretability of psychometrics, achieves a better performance of learning prediction and provides interpretability from three aspects: cognitive parameters, learner-resource response network, and weights of self-attention mechanism. Within the proposed framework, this paper presents a two-channel learning diagnosis mechanism LDM-ID as well as a three-channel learning diagnosis mechanism LDM-HMI. Experiments on two real-world datasets and a simulation dataset show that our method has higher accuracy in predicting learners’ performances compared with the state-of-the-art models and can provide valuable educational interpretability for applications such as precise learning resource recommendation and personalized learning tutoring in intelligent tutoring systems.