The previous studies on motivation have merely revealed the effects of gender, educational level, and country; however, the effect of the interactions between these variables on motivation has not yet been uncovered. The present study aims to statistically examine whether or not the interactions between these three variables can significantly impact the student science learning motivation. A set of the Science Motivation Questionnaire-II (SMQ-II) was administered to 867 Korean and 954 Indonesian secondary students (middle and high schools), and the Rasch analysis was performed to identify the validity and reliability of the instrument. To reveal the aim of this study, a three-way ANOVA and Pearson-correlation tests were used. Based on the findings, the interactions between country, gender, and educational level exerted significant effects on the student science learning motivation, as well as the remaining motivational components. The findings are discussed with respect to the factorial complexity that contributes to the student science learning motivation and the differences between the learning-motivation levels of the students of the two countries.