This study focused on how to enhance the interactivity and usefulness of augmented reality (AR) by integrating manipulative interactive tools with a real-world environment. A manipulative AR (MAR) system, which included 3D interactive models and manipulative aids, was designed and developed to teach the unit "Understanding Weather" in a natural science course, and to bridge a formal learning environment (i.e. school), non-formal (i.e. at a museum), and informal learning environments (i.e. home). Sixty-four sixth-grade students (12-13 years old) from four classes in Taipei City were enrolled in a seven-week general studies course entitled "Natural and Life Science and Technology", and they were divided into an experimental group (31 students who used the MAR system) and a control group (33 students who used multimedia teaching resources). After seven weeks of experiments, the results revealed that integrating the MAR system into inquiry-based field study made a greater positive impact on the students' academic achievement and motivation compared to the multimedia teaching resources installed on a tablet PC. Additionally, there were two interesting findings: (1) the MAR system offered effective learning materials relative to the multimedia teaching resources and (2) manipulative aids were an effective learning tool for interactivity and usefulness of AR. Besides, there were two meaningful suggestions associated with designing and developing the AR educational system for future researchers and designers, namely make it easy to use and include manipulative aids.