Swallowing is tightly coupled with emotion-autonomic states, while olfactory pathways project to limbic and hypothalamic hubs that can enhance parasympathetic activity and reduce stress. Whether a pleasant natural-wood odor can modulate swallowing-related brain activity and behavior remains unclear. To test whether Hinoki (Japanese cypress) inhalation improves affective ratings and increases the repetitive saliva swallowing test (RSST) difference (post-pre; swallows/30 s), and whether it suppresses swallowing-related activity in the premotor cortex (Brodman area 6 (BA6)) and the hypothalamus. The effects of exploratory whole-brain and interaction between Task and Odor were also evaluated. In a randomized within-subject crossover with a one-week interval, participants inhaled Hinoki essential oil or odorless rice-oil control. We assessed brain activity during voluntary saliva swallowing using functional magnetic resonance imaging (fMRI). Outcomes included subjective ratings (odor intensity, preference, comfort, recollection) and RSST counts per 30 s; RSST difference was computed as post-pre inhalation. Hinoki improved affective ratings and increased RSST difference compared to control. The odor main effect showed reduced activation in three regions-bilateral BA6 and the hypothalamus. An interaction effect between Task (swallowing vs. rest) and Odor (Hinoki vs. control) was found in the right putamen. The pattern supports a model: odor-induced autonomic calming (lower heart rate, reduced hypothalamic activity) lowers premotor load and improves swallowing, reflected in RSST difference. These findings suggest that aromatherapy-assisted dysphagia rehabilitation using olfactory priming-particularly for patients with post-stroke sequelae or post-stroke depression with poor appetite-may help enhance training efficiency and recovery.