Biopsychosocial models of children’s socioemotional development highlight the joint influences of physiological regulation and parenting practices. Both high and low levels of children’s baseline respiratory sinus arrhythmia (RSA) have been associated with children’s maladjustment, indicative of nonlinear associations. Negative or unsupportive parental responses to children’s emotions are consistently linked with internalizing (IP) and externalizing problems (EP), although few studies have examined how associations vary within families. This study examined within- and between-person associations of children’s quadratic baseline RSA, negative maternal emotion socialization, and children’s problems over six years. RSA was measured in 133 3.5-year-old children (72 female) in predominantly middle- to upper-middle socioeconomic status, Caucasian families. Mothers reported on their emotion socialization practices and their children’s adjustment concurrently and 1, 5, and 7 years later. Multilevel structural equation models revealed quadratic associations between baseline RSA and both IP and EP at the between-person level, suggesting that children with moderate RSA had fewer adjustment problems, on average, than children with lower or higher RSA. Across time and between families, children displayed more problems if their mothers reported more negative responses to their children’s emotions. Within families, IP were elevated on years when mothers reported higher than usual negative responses, and children with either high or low baseline RSA had more problems on years when mothers reported greater than usual negative responses to their children’s emotions. Altogether, these findings suggest that high and low baseline RSA may increase the risk for maladjustment, particularly in the time-varying context of aversive emotion socialization practices.