Background Emotional intelligence (EI) is increasingly recognized as an essential competency in medical education, yet evidence on its determinants and its relationship with mental health among Chinese medical students remains limited. This study examined factors associated with EI, explored its associations with stress, anxiety, and depression, and assessed whether EI mediates gender differences in psychological outcomes. Methods The study involved undergraduate medical students from the 1st, 3rd, 5th, 7th, and 9th semesters at the Norman Bethune Health Science Center of Jilin University. An online questionnaire was administered, including sociodemographic questions and validated scales to assess perceived stress, anxiety, depression, and EI. Additional data on factors such as leadership experience and participation in competitive activities were also collected. Descriptive statistics, t-tests, ANOVA, Pearson correlations, and multivariate logistic regression analyses were used to evaluate associations. Mediation analyses tested whether EI mediated the relationship between gender and mental health indicators. Results A total of 1,376 medical students were included (mean EI = 4.86 +/- 0.81). EI differed significantly by gender, academic semester, leadership experience, and competition participation (all p < 0.05). Students reporting stress (53%), anxiety (9%), or depression (18%) had markedly lower EI scores (all p < 0.001). Higher EI was independently associated with lower odds of stress (OR 0.20), anxiety (OR 0.14), and depression (OR 0.12) in adjusted models (all p < 0.001). Mediation analysis indicated that EI partially accounted for gender differences in psychological outcomes, explaining 36.4% of the total effect on anxiety and 38.3% on depression. These findings highlight the protective role of EI in medical students' mental health and its contribution to gender-related differences in psychological well-being. Conclusions EI plays a protective role in the mental health of medical students and partially explains gender disparities in anxiety and depression. As EI is a modifiable competency, incorporating EI-focused training, leadership development, and experiential learning into medical curricula may strengthen students' emotional skills and psychological resilience. Future longitudinal and multi-institutional studies are needed to evaluate the long-term impact of EI-enhancing strategies within medical education.