This research's aim was to explore the role of cognitive flexibility in mediating the effect of intrinsic motivation on the creativity of junior high school students. A creativity scale, an intrinsic motivation inventory and a cognitive flexibility inventory were utilized to investigate a sample of junior high school students in Shaanxi Province in western China. 765 valid questionnaires were collected and analyzed using the structural equation model (SEM). The SEM analysis showed that intrinsic motivation and cognitive flexibility have significantly positive impacts on junior high school students' creativity. Furthermore, a full model revealed that cognitive alternatives and cognitive control mediate the relationship intrinsic motivation and creativity, and the mediation effect of cognitive alternatives is significantly greater than that of cognitive control. In general, the current research suggests that the impact of intrinsic motivation on junior high school students' creativity is mediated by cognitive flexibility, and its results amplify prior scholars' research results and give educators an inspiration how to cultivate creativity for the middle school students.