Augmented reality (AR) recently shows great potential to facilitate students’ learning, especially their learning performance and motivation. However, few studies considered learners’ emotional factors such as learning anxiety, which may influence the learning results. This study aims to explore how different experimental conditions (AR & Non-AR) may affect the learning performance and motivation of students with different levels of learning anxiety. An AR-based magnetism experimental tool entitled “MagAR” was proposed to support junior high school students’ physics learning. The results indicated that, when compared to traditional experimental materials, AR can effectively improve students’ learning performance and motivation. Moreover, regardless of their anxiety, students in AR condition performed better on transfer test than those in Non-AR group. AR can also significantly motivate students with high anxiety. Besides, all students hold a positive attitude towards MagAR.