Maternal depressive symptoms are a crucial risk factor for children’s internalizing problems, though positive mother–child relationships may buffer this risk transmission. Mother–child physiological coregulation (e.g., synchrony) has emerged as a potentially important mechanism of developmental psychopathology and may play a role in the transmission of internalizing symptoms. In this two-wave longitudinal study, we examined whether and how mother–infant physiological synchrony (of respiratory sinus arrhythmia; RSA) moderated the association between maternal postnatal depressive symptoms and children’s internalizing problems in a rural, low-SES community sample (N = 166 dyads). At 6 months, mother–infant RSA synchrony and infant negative affect were assessed during free play. Mother reported their depressive symptoms at 6 months and children’s internalizing problems at 24 months. Multilevel structural equation models indicated that mother–infant dyads demonstrated significant and positive RSA synchrony on average and RSA synchrony significantly moderated the association between maternal depressive symptoms and children’s internalizing problems even after controlling for infant negative affect. Greater maternal depressive symptoms were associated with higher child internalizing problems when RSA synchrony was lower but not when it was higher. This finding suggests that mother–infant RSA synchrony may operate as a resilience factor for the intergenerational transmission of internalizing symptoms in community samples.