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Drawing on data from the 2022 Panel Study of Chinese University Students (PSCUS), this study investigates how cultural and economic capital are distinctly associated with undergraduates’ STEM major choices in China. The results indicate that: (1) Higher stocks of cultural capital are associated with a preference for non-STEM majors, whereas higher stocks of economic capital correlate with a greater likelihood of selecting STEM majors. (2) These associations are gendered. The correlation between cultural capital and non-STEM choice is pronounced among female students, while the association between economic capital and STEM choice is salient for male students. (3) Institutional prestige conditions these gendered pathways. The gendered patterns of capital are significant within ordinary higher education institutions, but are attenuated in elite HEIs (985 Project universities). These findings challenge the assumption of uniform family background effects on undergraduates’ major choice and highlight the gendered pathways through which capital is converted, offering new empirical evidence for gender inequality within China’s horizontally stratified higher education system.