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Augmented reality (AR) enables users to see virtual objects overlaid or synthesized in a real environment. Therefore, AR is a tool of auxiliary reality, and it reflects an environment of coexistence between reality and virtuality to users. Through the techniques of AR, provided specific images and dynamic effects of learning objects are overlaid at a defined position or symbol, users can interact with them to obtain more authentic sensation and experience interactive methods that are different from those in the past. In various subjects, the content of natural science courses is usually abstract, and contains concepts of high experimental operations. In ordinary and traditional teaching sites, teachers’ teaching method is usually the use of whiteboard writing or handheld teaching aids. Although this teaching method can provide students with specific object observation experiences, students may lack learning autonomy. Moreover, the operation of chemical experiments is risky, or some natural phenomena cannot be observed at any time or anyplace, thus, learners’ impression regarding such subjects cannot be enhanced. Many scholars suggested that, students use the same method and pace to engage in learning. However, not all students can develop an effective path that is beneficial to learning on their own, suggesting that, there are differences in the learning processes of different students (Lee, Cheng, Rai, and Depickere, 2005). As scientific concepts are complicated and highly technical, they are also subjects that are difficult to teach (Chen and Howard, 2010). This study intends to use the advantage of AR – being able to specifically reflect 3D objects – to develop a learning system of good interaction, as well as use cards/jigsaw to implement interactive game-based teaching. This study mainly used chemical experiments and earth sciences as the teaching content, and used the system to enable learners to operate cards to conduct experiments and observe natural phenomena that cannot be found in the textbooks of earth sciences. In recent years, an increasing number of studies on the influence of cognitive style on learners’ preference for the use of a learning system interface have been performed (Chen and Macredie, 2002; Clewley, Chen, and Liu, 2010). This study also introduced the issue of cognitive style in order to investigate whether there is any difference in usability perception and effectiveness of the use of the AR learning system by users of different styles. This study also investigated whether cognitive style affects learning motivation and effectiveness under the situation of different groupings. According to the said research background and motivation, the main purpose of this study is to integrate unmarked AR techniques with natural science courses to develop an e-learning system, and use image objects and 3D animation to stimulate sensory learning, in order to use this innovative information media to enhance students’ learning effectiveness and memory, and enrich their learning process. Afterwards, this study also intends to analyze and investigate the usability of this system. The study by Liu et al. (2009) indicated that, the problem-solving situation of media and cooperative learning can trigger students’ motivation and improve their learning effectiveness, and students’ level of e-application varies with their backgrounds (Wood and Howley, 2012; Zhong, 2011; Eynon, 2009). Appropriate learning and teaching materials cannot be determined until sufficient analyses are performed. A study also pointed out that an interactive e-media environment can meet the needs of cooperative learning (Tolentino et al., 2009). Based on the above, this study intends to investigate whether cognitive style affects users’ system usability perception, learning motivation, and self-perceived learning effectiveness as they operate this system to engage in cooperative learning, as well as to conduct experiments to further analyze and compare whether there is any difference in the various dimensions of different groups, in order to investigate the feasibility of the application of this system for learners with different cognitive styles.