Dental malocclusions are common and often underdiagnosed situations in dogs, which might result in oral trauma, impaired mastication, and periodontal disease. Nevertheless, scientific investigations into breed-specific variations in dentition remain scarce. To evaluate breed-specific dental variations in dogs, a retrospective cross-sectional analysis was conducted on 92 clinical canine head computed tomography (CT) scans obtained in Chengdu, China, representing a range of breeds and skull morphologies. Dental alignment and occlusal relationships were calculated using standardized malocclusion classification criteria. As a result, malocclusions were found and identified in 46.7% of dogs. Among them, brachycephalic breeds indicated a high prevalence of malocclusion, with Shiba Inu dogs demonstrating the highest malocclusion rate (66.7%), whereas Golden Retrievers and Akitas showed the lowest prevalence (16.7%). Class I malocclusions characterized by dental crowding were most common (44.19%), followed by Class II malocclusions (overbite) (30.23%), and Class III malocclusions (underbite) (20.93%). Our findings demonstrated a strong association between skull morphology and dental alignment abnormalities.