Learner behaviours often provide critical clues about learners' cognitive processes. However, the capacity of human intelligence to comprehend and intervene in learners' cognitive processes is often constrained by the subjective nature of human evaluation and the challenges of maintaining consistency and scalability. The recent widespread AI technology has been applied to learning analytics (LA), aiming at a more accurate, consistent and scalable understanding of learning to compensate for challenges that human intelligence faces. However, machine intelligence has been criticized for lacking contextual understanding and difficulties dealing with complex human emotions and social cues. In this work, we aim to understand learners' internal cognitive processes based on the external behavioural cues of learners in a digital reading context, using a hybrid intelligence (HI) approach, bridging human and machine intelligence. Based on the behavioural frameworks and the insights from human experts, we scope specific behavioural cues that are known to be relevant to learners' attention regulation, which is highly relevant for learners' cognitive processes. We utilize the public WEDAR dataset with 30 subjects' video data, behaviour annotation and pre--post tests on multiple choice and summarization tasks. We apply the explainable AI (XAI) approach to train the machine learning model so that human evaluators can also understand which behavioural features were essential for predicting the usage of the cognitive processes (ie, higher-order thinking skills [HOTS] and lower-order thinking skills [LOTS]) of learners, providing insights for the next-round feature engineering and intervention design. The result indicates that the dominant use of attention regulation behaviours is a reliable indicator of low use of LOTS with 79.33% prediction accuracy, while reading speed is a valuable indicator for predicting the overall usage of HOTS and LOTS, ranging from 60.66% to 78.66% accuracy, highly surpassing random guess of 33.33%. Our study demonstrates how various combinations of behavioural features supported by HI can inform learners' cognitive processes accurately and interpretably, integrating human and machine intelligence.