To propose a novel classification system for stratifying coronal curve patterns in congenital cervicothoracic scoliosis with hemivertebrae (CTS-HV). Type A: regional cervicothoracic deformity only disturbing the balance of head-neck-shoulder complex; Type B: cervicothoracic deformity with significant trunk tilt to the convex side; Type C: cervicothoracic deformity with a significant compensatory thoracic curve. The reliability and reproducibility were assessed via the Kappa test. The differences among different subtypes in deformity parameters and bony structures were compared to identify the causative factors predisposing to different subtypes. 98 patients were classified into Type A (47 cases), Type B (31 cases), and Type C (20 cases). The Kappa test showed excellent reliability (Kappa value = 0.847) and reproducibility (Kappa value = 0.881). The proportions of Klippel-Feil syndrome in Types B (71.0%) and C (85.0%) were significantly higher than in Type A (46.8%; all P < 0.05). Type A (66.0%) and Type B (71.0%) predominantly had their hemivertebra (HV) at T3 or T4, while Type C (75%) mostly had HV at T1 or T2. Type B exhibited the most severe trunk tilt, head shift, neck tilt, head tilt, and coronal balance distance (all P < 0.05). Type C had the lowest T1 tilt and first rib angle despite the greatest cervicothoracic Cobb angle (all P < 0.05). This novel reliable classification allows a better understanding of structural diversity and different coronal compensatory mechanisms for the natural progression of CTS-HV. It can contribute to determining the individualized treatment strategy and standardizing academic communication for this rare clinical entity.