The microscopic composition of substances is a piece of essential but abstract knowledge in chemistry. Junior high school students may experience difficulty in mental representation when learning micro concepts, which leads to problems such as unsatisfactory academic performance and low learning motivation. Augmented reality (AR) is an optimal choice for presenting abstract concepts and invisible phenomena. Consequently, this study developed an AR application including three-layer experiential learning activities and integrating multiple external representations (text, pictures, 3D models, operations, etc.). To assess the effect of the AR application on students' knowledge gains, learning motivation, and technology perception, an experiment was conducted with 95 ninth-grade students aged 13-15 years who were randomly assigned to two groups (AR and non-AR). The results show that the AR application helped increase students' knowledge gains. Although there was no significant difference in the retention test between the two groups, scores on the transfer test were significantly higher for the AR group than for the non-AR group. Moreover, the AR application significantly improved students' motivation to learn. Finally, students had a positive perception of AR technology.