<p>Previous research has consistently shown that students have higher learning interests, attitudes, and motivation toward science in elementary school compared to middle and high school. However, the key predictors behind the observed differences in engagement levels across grade levels remain unclear. This study aims to identify the association between students’ perceptions of science instruction and their emotional engagement, as well as to examine the differences across various educational stages. A 2-level organizational multilevel model was employed to investigate this association. In addition, the analysis examined whether the associations varied between grade levels. A sample of 6465 students from 3rd grade to 12th grade from 25 schools participated in the study. This study shows that students in higher grades have significantly lower emotional engagement comparedar to third-grade students. Findings reveal significant associations between students’ perceptions of science instruction, both in perceiving it as interesting and understandable, and their emotional engagement in science learning. There is a greater increase in students’ emotional engagement in a transition year (i.e., sixth grade) when they perceive science class as interesting than in other grades. There were no statistically significant differences between grades in students’ perception of science as understandable and emotional engagement. This study provides evidence of the importance of delivering interesting and well-designed science classes.</p>