Background <p>The elevated prevalence of depression among left-behind children is influenced by parent-child alienation. Gender differences may exist in both depression symptoms and parent-child alienation. This study employs undirected and directed network comparative analysis to explore gender disparities in parent-child alienation and its association with depression symptoms among left-behind children, offering nuanced data support for clinical decision-making.</p> Methods <p>A self-reported questionnaire assessing parent-child alienation and depressive symptoms was completed by 1,833 left-behind children (55.9% male, 44.1% female; mean age = 14.60 ± 2.13, range = 9–18 years). Descriptive statistics, Gaussian graphical models (GGM) and Bayesian directed acyclic graphs (DAG) were used to examine gender differences in network structures and directional relationships.</p> Results <p>The prevalence of depression among male left-behind children was 19.73%, while among females it was 28.06%. Females reported higher total scores of parent-child alienation compared to males (34.55 vs. 31.79). “Reluctance to ask parents for money” may be a primary factor contributing to parent-child alienation among left-behind children. Maternal alienation exhibits a stronger association with depressive symptoms. Network comparison revealed no significant differences in network structure and global invariance, but significant disparities were found in some edges and nodes. Bayesian network similarity was 22%, with a directional consistency of 45%. Depression symptoms among left-behind children may be a factor leading to parent-child alienation.</p> Conclusion <p>Although no significant overall gender differences were found in network structures, subtle disparities existed in edge strengths and directional patterns. The findings suggest potential associations from depressive symptoms to parent-child alienation, informing prevention strategies and targeted research.</p>