The purpose of this study was to use magnetic resonance imaging (MRI) to compare the volumes and three-dimensional configurations of the soft palate and nasopharynx in non-brachycephalic and brachycephalic dogs with different body weights, and infer which factors influence nasopharyngeal volume. This was a retrospective observational study. The brain MRI medical records of all dogs referred to the Veterinary Medical Center, Chungbuk National University, between 2013 and 2016, for evaluation of intracranial disease were reviewed. There was a significant difference in the two-dimensional parameters including soft palate length/skull length ratio (P<0.01) and maximum soft palate thickness (P<0.01), and three-dimensional parameters which included soft palate volume (P<0.01), nasopharyngeal volume (P<0.01), soft palate/total upper airway volume ratio (P<0.01), and nasopharyngeal volume/total upper airway volume ratio (P<0.01), between brachycephalic and non-brachycephalic dog breeds. Nasopharyngeal volume correlated positively with the maximum soft palate thickness and body weight in all breeds. The three-dimensional morphologic grades of soft palate were significantly different between the two groups. In brachycephalic breeds, Grade 3 was observed in 33% of cases but was absent in non-brachycephalic breeds, where Grade 1 was present in 85% of the cases. We can conclude that three-dimensional morphology and upper airway volume are significantly different between brachycephalic and non-brachycephalic breeds, and body weight and maximum soft palate thickness are the key factors associated with a decreased nasopharyngeal volume.