To examine the swallowing characteristics in patients with mild cognitive impairment (MCI) and dysphagia risk and explore brain activity changes using regional homogeneity (ReHo) with resting-state functional magnetic resonance imaging (rs-fMRI). We included 28 patients with MCI and dysphagia risk and 17 age-matched older adults. All participants underwent neurological, cognitive examinations, and a videofluoroscopic swallowing study (VFSS). We quantitatively analyzed the VFSS temporal and kinetic parameters of the 5- and 10-mL swallows. The participants underwent rs-fMRI, and the ReHo values were calculated. Differences in the swallowing physiology and rs-fMRI findings between participants with MCI and controls were analyzed. Correlation analyses were also conducted. Compared to the control group, patients with MCI and dysphagia risk had lower global cognition scores, longer 10-mL oral transit times (OTTs), and lower executive function scores. ReHo in the bilateral inferior occipital lobes (IOLs) and left prefrontal lobe decreased in patients with MCI and dysphagia risk compared to participants in the control group. In patients with MCI, the 10-mL OTT was negatively correlated with the Montreal Cognitive Assessment (MoCA) score, and the ReHo values were positive correlated with quantitative temporal swallowing measurements using canonical correlation analysis. Mediation analysis revealed that the ReHo values of the left and right IOL acted as significant mediators between the MoCA score and the 10-mL OTT. We found that individuals with MCI and dysphagia risk, verified by reduced MoCA scores, demonstrated prolonged OTTs when swallowing larger boluses compared with age-matched controls. There was a negative correlation between the MoCA score and 10-mL OTT, which was partially mediated by the left and right IOL ReHo values, suggesting that functional changes in the IOLs and left prefrontal lobe associated with oral swallowing status and cognitive level in individuals with MCI and dysphagia risk.