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Given that gender differences in higher education opportunities are narrowing in China, this paper studies the pattern of gender gaps in the horizontal stratification of higher education. Analyzing the 2020 Panel Study of Chinese University Students (PSCUS) data, we find that (1) significant gender gaps exist in the horizontal stratification of higher education in China. Compared to women, men are more likely to attend high-tier institutions and are more likely to choose STEM majors than non-STEM majors. (2) Gender gaps in tiers of higher education institutions are moderated by structural factors. Men’s advantages in attending high-tier institutions are more significant for students from rural areas and those with lower socioeconomic backgrounds. (3) Gender gaps in majors are adjusted by cultural factors. Gender disparities in choosing STEM and non-STEM majors are more significant for students with traditional gender-role attitudes than those with egalitarian gender attitudes. The findings shed new light on understanding gender gaps in higher education in contemporary China.