Online learning methods become an important element in supporting the flexibility and effectiveness of teaching and learning process, especially through approaches such as Video Tutorial, Virtual Discussion, and Self-paced Reading. This research aims to evaluate the effectiveness of the three methods in improving students' engagement, comprehension, and learning motivation by utilizing Naive Bayes algorithm. The dataset used includes student data taken through questionnaires and teacher evaluation results, with variables such as material suitability, engagement, ease of access, and student exam results. Through this approach, the research is able to predict the learning method that best suits students' needs based on the analyzed variables. The results show that Video Tutorial is the most effective method in supporting students' understanding and motivation. The implementation of this research is expected to help the development of a better online learning system in improving students' learning experience, and provide practical recommendations for educators in choosing the right learning method.