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This study examined gender-based developmental patterns in social and emotional skills among 16,148 Chinese secondary students using Latent Profile Analysis (LPA), and explored their associations with demographics and academic literacy in math, reading, and science. Results identified four profiles for girls—average (11%), good (60%), unbalanced (12%), and high (17%)—and three for boys—average (33%), good (58%), and high (9%). These patterns were significantly associated with region, grade level, and family socioeconomic and cultural status. Moreover, academic literacy scores varied significantly across profiles. The findings highlight distinct developmental trajectories between genders and underscore the need for tailored interventions to support students’ social and emotional development based on profile characteristics.