Background: While trait emotional intelligence (EI) has been found to be related to young adolescents' affect, the underlying mechanisms need to be further explored. Previous findings are also limited by common method problems arising from the use of cross-sectional design involving single-wave data capture. Objective: The study aims to clarify the relation between trait EI and young adolescents' positive and negative affect by further exploring the mediating roles of personal resilience, social support, and prosocial behavior. Method: We conducted a three-wave survey among 714 Chinese junior high school students (mean age of 11.11 years) with temporal separations of the research measures to reduce common method variance. Trait EI was measured at the beginning of Grade 6; personal resilience, social support, and prosocial behavior were measured at the end of Grade 6; positive and negative affect were measured at the end of Grade 7. Results: Trait EI at the beginning of Grade 6 was positively related to positive affect and negatively related to negative affect by the end of Grade 7. The influence of trait EI on positive affect was fully mediated by personal resilience, social support, and prosocial behavior at the end of Grade 6. Its influence on negative affect was also fully mediated by social support. Conclusions: The findings clarify the mechanisms underlying the trait EI effect and highlight the importance of future youth programs targeting mediation mechanisms. In particular, we suggest the worth of utilizing trait EI to better facilitate personal and social resources when facing difficulties, and to help others in appropriate and effective ways.