Material structures and chemical equilibrium are important learning units in high school chemistry. In this study, an augmented reality (AR) system is developed to assist high school students in learning chemistry. Students can use AR cards to conduct virtual chemistry experiments, and the submicroscopic view of a chemical reaction will be displayed according to the chemical equation specified by the reactants and coefficients on AR cards. They can change the AR cards to observe the experimental results and obtain the simplest integer ratio in a chemical equation. It is helpful for understanding that a chemical reaction changes the composition of reactants to form new products and that the process obeys the law of conservation of mass. Empirical research has been conducted in which the experimental group used the AR system and the control group used the traditional teaching method for learning chemistry. The analytical results show that the AR system is more effective than the traditional teaching method, especially for low-achievement students. The questionnaire results indicate that the learning motivation of the experimental group was slightly higher than that of the control group, and the cognitive load was slightly lower than that of the control group, both without achieving a significant difference