The availability of educational data in novel ways and formats brings new opportunities to students with special education needs (SEN), whose behaviour and learning are highly sensitive to their body conditions and surrounding environments. Multimodal learning analytics (MMLA) captures learner and learning environment data in various modalities and analyses them to explain the underlying educational insights. In this work, we applied MMLA to predict SEN students’ behaviour change upon their participation in applied behaviour analysis (ABA) therapies, where ABA therapy is an intervention in special education that aims at treating behavioural problems and fostering positive behaviour changes. Here we show that by inputting multimodal educational data, our machine learning models and deep neural network can predict SEN students’ behaviour change with optimum performance of 98% accuracy and 97% precision. We also demonstrate how environmental, psychological, and motion sensor data can significantly improve the statistical performance of predictive models with only traditional educational data. Our work has been applied to the Integrated Intelligent Intervention Learning (3I Learning) System, enhancing intensive ABA therapies for over 500 SEN students in Hong Kong and Singapore since 2020. Copyright © 2023 IEEE.