This study aims to investigate the motivation for science learning of 3rd year high school students who choose different majors from their track. A total of 2,012 high school 3rd year students participated in this study. We used Science Motivation Questionnaire Ⅱ (Glynn et al., 2011) to measure the students' science motivation and performed Rasch analysis, MANOVA and logistic regression analysis. First, results showed that 11.5% of students in the science track switched their pathway to a non-STEM major and 14.3% of students in the humanities track switched to a STEM major. In addition, there were gender differences in switching majors. Second, we found a significant difference in science motivation between two groups of students switching their major only in career motivation. Third, science motivation was the significant predictor of STEM major choice; in particular, career motivation was the most influential variable. Based on these results, we proposed that prediction of and paying close attention to students' career motivation are required before making decisions on which track to take.