The notion of science identity has been widely discussed in the field of science education in recent years. Many research studies have focused on students’ science identity in a general sense in spite of the fact that students are usually exposed to discipline-specific science courses in high school. We argue that it is more appropriate to explore high school students’ disciplinary identities in natural sciences (i.e. physics, chemistry and biology). A quantitative approach was used to investigate high school students’ disciplinary identities among three science subjects and explore the effects of these identities on students’ intentions to major in college science programs. An instrument addressing three disciplinary identities was administered to 510 students from 10 science classes in seven high schools in Guangzhou, the capital of Guangdong, China. The major findings indicate that high school students had the lowest identity in physics among the three disciplines. Moreover, physics identity was found to be a significant indicator that had the strongest effect on students’ intentions to choose science-related college programs, while biology identity was a non-significant indicator with the weakest effect on intended selection of a college science program. The results of this study have practical implications for enhancing high school students’ science identities.