This paper attempts to explore the role of non-cognitive abilities in explaining the apparent phenomenon of female advantage in Chinese universities. The results showed that female students significantly outperformed their male counterparts in both academic and non-academic performance. This advantage is robustly present in samples among different majors or level-tiered universities, and especially large in samples from humanities and social majors as well as non-key universities. Compared to male students, female students have higher levels of non-cognitive ability in conscientiousness, achievement motivation, extroversion, and emotional stability; but they have lower levels of self-confidence and lower return rates of conscientiousness, achievement motivation, and self-confidence about educational achievement. Non-cognitive abilities have been shown to play a mediating role in the formation of female dominance in school performance. The decomposition results suggest that higher levels of non-cognitive ability are the main cause of educational advantage for women, especially in terms of non-academic performance. The findings provide a new perspective on understanding the phenomenon of gender stratification in higher education and have practical implications for optimizing university policies.