This study investigates the effect of structuring cooperative learning based on conceptual change approach on grade 9 students' understanding the concepts of mixtures and their motivation, compared with traditional instruction. Among six classes of a high school, two of them were randomly assigned to cooperative learning group where students were instructed by Cooperative Learning based on Conceptual Change (CLCC), the other two classes were randomly assigned to traditional learning group where students were instructed by Cooperative Learning based on Conceptual Change without well-structuring the basics of cooperative learning (CLCC(-)), and the remaining two classes were randomly assigned to control group where students were instructed by Traditional Instruction (TI). Mixtures Concept Test (MCT), motivation section of Motivated Strategies for Learning Questionnaire (MSLQ) except goal orientation sub-scales, and Achievement Goal Questionnaire (AGQ) were assigned to the sampled students before treatments are commenced as pretests and after treatments are completed as post-tests. According to post-test scores, there were statistically significant mean differences among the groups exposed to variations of cooperative learning based on conceptual change and traditional instruction with respect to students' understanding the concepts of mixtures and their motivation. Results drawn upon this study revealed specifically that students exposed to CLCC had better understanding and lower alternative conceptions about the concepts of mixtures, perceived contents related to chemistry more valuable, felt greater control over their own learning, dealt better with sense of worry and emotionality during tests, adapted performance avoidance goals less, and mastery approach goals more than students instructed by CLCC(-) and TI.