The Model of Neurovisceral Integration suggests that vagally mediated heart rate variability (vmHRV) represents a psychophysiological index of inhibitory control and thus, is associated with emotion regulation capacity. Over the past decade, growing empirical evidence supports this notion, showing that those with higher resting vmHRV can regulate negative emotions more adequately. However, to our knowledge, no study has previously examined how resting vmHRV may relate to everyday perceived difficulties in emotion regulation. The present study attempts to examine such relationship in 183 undergraduate students (98 female, 60 minority, mean Age = 19.34). Resting vmHRV was collected during a 5-min resting baseline period, and everyday difficulties in emotion regulation were assessed using the Difficulties in Emotion Regulation Scale (DERS). Controlling for potential covariates (including both trait anxiety and rumination), results revealed a negative relationship between resting vmHRV and DERS such that lower resting vmHRV was associated with greater difficulties in emotional regulation, especially a lack of emotional clarity and impulse control, as indicated by the respective subscales of the DERS. These findings provide further evidence for the Neurovisceral Integration Model, suggesting that emotion regulation and autonomic regulation share neural networks within the brain. Moreover, the present study extends prior research by highlighting two distinct facets of emotion regulation (impulse control and emotional clarity) that should be of particular interest when investigating the link between emotion regulation, resting vmHRV, and related health outcomes including morbidity and mortality.