The purpose of this study is to identify changes in cognitive, affective, and social achievement following enrollment in Busan innovative schools, and to analyze the effects of student- and school-level factors on these changes. To do this, propensity score matching and multilevel modeling were adapted to the Busan Educational Longitudinal Study (BELS) data from the 1st to 5th wave (4th to 8th grades). The results were as follows. As the grade level increased, students Korean, math, and English academic achievements were found to increase, and school happiness decreased. However, the growth rate in sense of community was not statistically significant. In the initial stage (4th grade) for math academic achievement and school happiness, there was a significant difference between innovative schools and general schools, with both being significantly lower in innovative schools than in general schools. On the other hand, there was no significant difference between innovative schools and general schools in the initial stage in the growth rate of Korean and English academic achievement and sense of community. Various other student- and school-level factors were found to have significant effects on the initial stage and the growth rate of academic achievement, school happiness, and sense of community. Based on the findings, implications of this study and suggestions are discussed.