This analysis compared the structures of affective factors which influence the achievement of science between elementary and lower secondary school students. The data used for this analysis is the survey of curriculum implementation conducted by the National Institute for Educational Policy Research. By analyzing the student questionnaire, I extracted five constructs "preference to science" "usefulness of science" "usefulness for examination" "usefulness for career" and "attitude toward thinking in the experiment". The results of structural equation modeling presented the difference in effects on the achievement of science between elementary and lower secondary school students.