Augmented Reality (AR) has emerged in our educational paradigm as a new tool to accelerate change in the teaching and learning process. This technology can improve students' visualisation skills, which helps them understand abstract concepts, especially in Chemistry. Furthermore, visualisation skills help improve students' critical thinking. This study was conducted with 16 secondary students. Before and after the intervention, students were required to complete a Purdue Spatial Visualisation Test to measure their visualisation skills. During four weeks of intervention, students explored the content using a mobile augmented reality application for learning chemical bonds (called CBOND) and completed critical thinking tasks each week. This study employed data mining using a decision tree to predict the path to improving students' visualisation and critical thinking skills in learning chemical bonds. The results revealed that CBOND had a significant effect on students' visualisation and critical thinking development. Therefore, this study proved that augmented reality technology could help students to visualise abstract concepts, especially in Chemistry, and in turn, foster their higher level of critical thinking.