The purpose of this study is to examine the effects of employing an augmented reality (AR) lens imaging system on inquiry-based learning concerning junior high school students' science achievement, science learning motivation, and inquiry skills. For this purpose, an AR lens imaging learning system was developed specifically for the lens imaging unit. A quasi-experimental design was utilized comprising an experimental group and a control group. The participants included 60 eighth-grade students from two classes in a junior high school in Taiwan. One class, consisting of 30 students, was assigned as the experimental group and utilized an AR lens imaging learning system for inquiry-based learning. The other class, also consisting of 30 students, served as the control group and utilized traditional lens imaging devices for inquiry-based learning. The instructional duration comprised two sessions totaling 90 min. The study's results revealed that implementing the AR lens imaging learning system for inquiry-based learning resulted in improvements in overall science achievement in the lens imaging unit. Additionally, individual science achievement was enhanced in the convex and concave lens imaging topics. Furthermore, the AR lens imaging learning system increased students' motivation for science learning. It also enhanced students' specific inquiry skills in the concave lens imaging topic, such as observation and analysis and discovery. However, no enhancement was observed in inquiry skills for the convex lens imaging topic.