Dental malocclusion is a potential contributor to chronic systemic distress; however, its underlying neural mechanisms remain unclear. This study investigated acute autonomic responses during and after tooth grinding under both appropriate and inappropriate occlusal conditions. Seventeen healthy young adults underwent tooth grinding using removable metal overlays attached to either the canines or first molars in randomized order to simulate the two occlusal dental conditions. Autonomic nervous activity was assessed by heart rate variability (HRV) analysis of electrocardiogram signals and pupillary light reflex (PLR) responses. Masseter muscle activity was recorded using surface electromyography (EMG). Both occlusal dental conditions resulted in a significant increase in EMG activity compared with the baseline resting state (p < 0.01). However, no significant differences were observed between the two occlusal conditions. HRV analysis revealed that tooth grinding significantly suppressed the parasympathetic activity compared with baseline in both occlusal conditions (p < 0.01), with no significant differences between them. Notably, a prolonged pupil redilation time following tooth grinding was observed only under inappropriate occlusal conditions relative to baseline (p < 0.01). Occlusion-specific changes in PLR were evident only under blue light stimulation, suggesting the utility of blue light as a neurological probe for melanopsin-containing intrinsically photosensitive retinal ganglion cells. These findings indicate that sympathetic recovery after grinding is diminished under malocclusion compared with natural occlusion. This altered autonomic balance may explain the association between dental malocclusions and psychological stress.