Examining the changes in students who have undergone integrated education and providing appropriate follow-up measures is crucial for enhancing educational effectiveness. This exploratory study aims to analyze the impact of perceptions of MESA/STEM education on science motivation among students in the United States and Korea, based on ethnic differences, and to derive relevant implications. Data from 202 students who received MESA/ STEM education in the U.S. and Korea were utilized for the study. Rather than comparing the two countries, the study focused on examining the effects based on ethnic differences using regression analysis and a one-level multilevel model analysis, and comparing the results to derive implications. The study found the following results: First, there was a significant correlation between the two test scores, and regression analysis confirmed that perceptions of MESA/STEM education significantly influenced science motivation. Second, comparing the regression equations based on ethnicity revealed that the intercept and slope varied by ethnicity. This led to the design and implementation of a one-level multilevel model analysis. Significant results were found in the random effects of the intercept, and the fixed effects of the independent variables showed that perceptions of MESA/STEM education accounted for approximately 33% of the total variance in science motivation among ethnic groups. Given the increasing number of multicultural students not only in the U.S. but also in Korea, various ethnicities are becoming educational targets. The findings of this study can provide discussion points for estimating the educational effects on various student groups and for the formulation and implementation of policies that reflect these effects.