Increasing urbanization, unemployment, and better employment opportunities drive millions of people to migrate between states and cities in many developing countries, including India. For primary breadwinners, labor migration is a common strategy to cope with poverty, often leaving small children at home. This migration poses significant physical and mental health challenges for left-behind children (LBC). This study, using a multi-stage convenience sampling of 966 children (aged 6–14 years) from the rural eastern region of India (450 from migrant families, 516 from non-migrant families), compares the psychosocial well-being of LBC with non-left-behind children (NLBC). The study assesses children’s health-related quality of life, focusing on emotional and psychological health disorders. Psychometric screening tools were used to evaluate emotional and behavioral disorders (30 items) and anxiety and depression (25 items). The findings reveal that parental migration negatively impacts the psychological well-being of children. Binary logistic regression models indicate that LBCs are more likely to experience emotional and behavioral disorders than NLBCs (AOR: 2.07; 95% CI: 1.73–5.96; P < 0.05). Similarly, LBCs are more likely to develop anxiety and depression (AOR: 2.12; 95% CI: 0.73–4.33; P < 0.01). The duration of parental migration significantly influences children’s emotional and anxiety disorders. A thorough assessment is crucial to identify vulnerable rural children, address their needs, and implement effective health interventions.