The main purpose of this study was to investigate the effects of cooperative learning based on conceptual change approach instruction on ninth-grade students' understanding in chemical bonding concepts compared to traditional instruction. Seventy-two ninth-grade students from two intact chemistry classes taught by the same teacher in a public high school participated in the study. The classes were randomly assigned as the experimental and control group. The control group (N = 35) was taught by traditional instruction while the experimental group (N = 37) was taught cooperative learning based on conceptual change approach instruction. Chemical Bonding Concept Test (CBCT) was used as pre- and post-test to define students' understanding of chemical bonding concepts. After treatment, students' interviews were conducted to observe more information about their responses. Moreover, students from experimental groups were interviewed to obtain information about students' perceptions on cooperative work experiences. The results from ANCOVA showed that cooperative learning based on conceptual change approach instruction led to better acquisition of scientific conceptions related to chemical bonding concepts than traditional instruction. Interview results demonstrated that the students in the experimental group had better understanding and fewer misconceptions in chemical bonding concepts than those in the control group. Moreover, interviews about treatment indicated that this treatment helped students' learning and increased their learning motivation and their social skills.