This study examined to what extent experiences in innovation schools have an interrelationship between elementary school and middle school education and analyzed how the connectivity had an impact on students academic performance. Using 1－6 data of the Gyeonggi Education Panel Study (GEPS), the students were divided into four groups based on the type of schools they attended. Before comparing academic achievements between treatment and control groups, propensity score matching methods were utilized to control for potential selection bias among students in the four groups. According to the analysis, even though more than 60% of the graduates of innovation elementary schools wanted to go to innovation middle schools, only about 40% of them actually did so. This confirms that the linkage of innovation education between school levels does not work appropriately. Moreover, it was revealed that students who attended innovation elementary and middle schools consecutively considered the degree of student-centered learning comparatively high, and the degree of reduction in intrinsic learning motivation was significantly small. Lastly, the linkage of innovation education had several positive effects on academic performance. Based on these findings, this study emphasizes the significance of continuity in innovation education between school levels and suggests relevant alternatives.