Herein, we developed a mobile augmented reality (AR) application that can recognize chemical bonding by arranging markers on which atoms are augmented, in accordance with the specific characteristics of actual chemical bonding. From an educational affordance perspective, the development targets for AR application were selected to recognize chemical bonding, and the AR application was designed to reflect cognitive, sensory, and physical affordances. Further, a usability attitude test and pre- and post-tests of academic achievement, learning flow, and science learning motivation were conducted. After investigating the usability attitude of the AR application, we confirmed that users' perceptions of its usefulness and enjoyment significantly influence their intention to use the application. The post-test results reveal that academic achievement, learning flow, and science learning motivation improved after using the AR application. This study suggests that the developed AR application can serve as a learning tool that enhances understanding regarding chemical bonding and fosters interest in learning.