Background <p>The mental health of left-behind children in China has become a core societal concern. This study examines the impact of school empowerment on the mental health of left-behind children through the internal pathway of psychological empowerment, aiming to address the gap in existing research on the “environment-psychology” interaction mechanism.</p> Methods <p>A questionnaire survey was conducted among 317 left-behind children in Yunnan Province, China. The School Empowerment Scale, Psychological Empowerment Scale, and Mental Health Scale were used for measurement, and the mediator model was tested using Model 4 of SPSS PROCESS.</p> Results <p>Among the left-behind children sample in this study, school empowerment exerted a direct positive impact on mental health; psychological empowerment demonstrated a substantial partial mediating effect (49.015%) between school empowerment and mental health, indicating that nearly half of the total effect of school empowerment on mental health was transmitted via psychological empowerment. Additionally, both the direct path of school empowerment to mental health and the indirect path through psychological empowerment exhibited stronger explanatory power in left-behind children compared to non-left-behind children (direct path R²: 0.206&gt;0.180; mediation model R²: 0.374&gt;0.340). Psychological empowerment also showed a more pronounced explanatory role in left-behind children (R²: 0.226&gt;0.214).</p> Conclusion <p>This study validates the pathway of “school empowerment influencing psychological empowerment, which in turn affects mental health” among left-behind children in China. The findings not only expand the application of empowerment theory in non-Western contexts but also provide an actionable practical framework for mental health education for left-behind children in China.</p>