Neurobiological and social-contextual influences shape children’s adjustment, yet limited biopsychosocial studies have integrated temporal features when modeling physiological regulation of emotion. This study explored whether a common underlying pattern of non-linear change in respiratory sinus arrhythmia (RSA) across emotional scenarios characterized 4–6 year-old children’s parasympathetic reactivity (N = 180). Additionally, we tested whether dynamic RSA reactivity was an index of neurobiological susceptibility or a diathesis in the association between socioeconomic status, authoritarian parenting, and the development of externalizing problems (EP) and internalizing problems over two years. There was a shared RSA pattern across all emotions, characterized by more initial RSA suppression and a subsequent return toward baseline, which we call vagal flexibility (VF). VF interacted with parenting to predict EP. More authoritarian parenting predicted increased EP two years later only when VF was low; conversely, when VF was very high, authoritarian mothers reported that their children had fewer EP. Altogether, children’s patterns of dynamic RSA change to negative emotions can be characterized by a higher order factor, and the nature by which VF contributes to EP depends on maternal socialization practices, with low VF augmenting and high VF buffering children against the effects of authoritarian parenting.