Introduction: Music is ubiquitous and powerful in the world's cultures. Music listening involves abundant information processing (e.g., pitch, rhythm) in the central nervous system and can also induce changes in the physiology, such as heart rate and perspiration. Yet, previous studies tended to examine music information processing in the brain separately from physiological changes. In the current study, we focused on the temporal structure of music (i.e., beat and meter) and examined the physiology, neural processing, and, most importantly, the relation between the two areas. Methods: Simultaneous MEG and ECG data were collected from a group of adults (N = 15) while they passively listened to duple and triple rhythmic patterns. To characterize physiology, we measured heart rate variability (HRV), indexing the parasympathetic nervous system function (PSNS). To characterize neural processing of beat and meter, we examined the neural entertainment and calculated the beat-tometer ratio to index the relation between beat-level and meter-level entrainment. Specifically, the current study investigated three related questions: (a) whether listening to musical rhythms affects HRV; (b) whether the neural beat-to-meter ratio differed between metrical conditions, and (c) whether neural beat-to-meter ratio is related to HRV. Results: Results suggest that while at the group level, both HRV and neural processing are highly similar across metrical conditions, at the individual level, neural beat-tometer ratio significantly predicts HRV, establishing a neural-physiological link. Conclusion: This observed link is discussed under the theoretical "neurovisceral integration model," and it provides important new perspectives in music cognition and auditory neuroscience research.