Respiratory sinus arrhythmia (RSA) is a biomarker of mental health, but RSA‐symptom relations in parents of young children are understudied. We examined how anxiety symptoms, depressive symptoms, resting RSA, and RSA reactivity during challenging parent–child interactions clustered in a community sample of mothers (N = 126) and fathers (N = 87) of 3‐year‐olds and whether profiles predicted child emotional and behavioral dysregulation at age 4. Mothers fit four profiles (Typical, Mild Risk, Moderate Risk/Withdrawal, and Moderate Risk/Augmentation), suggesting that RSA reactivity was distinct by predominant symptom type at higher levels of risk: specifically, heightened RSA withdrawal was associated with a higher probability of anxiety symptoms and RSA augmentation was associated with a higher probability of depressive symptoms. Fathers fit three profiles (Typical, Mild Risk, and Moderate Risk) where Moderate Risk was characterized by RSA augmentation and a higher probability of both anxiety and depressive symptoms. Mild risk profiles showed heightened resting RSA for mothers and fathers but no differences in RSA reactivity. Both mild and moderate risk profiles predicted higher child dysregulation 1 year later compared to typical profiles. Findings offer preliminary evidence that parasympathetic physiology covaries with symptoms differently for mothers and fathers and that parental profiles of physiology and symptoms inform children's developmental psychopathology.