This article aimed to explore the correlation between the periorbital morphology determined using a 3D scanning system and CT in congenital microphthalmia.Fifty-two children with microphthalmia aged 0-6 were enrolled in this study. All the participants were subjected to orbital CT scans and 3D scanning. The CT and 3D scanning images were separately processed to obtain the orbital and facial parameters. Multivariate regression was used to analyze the correlation between 3D parameters and orbital volume.The orbital volume of the affected side (15.25 ± 3.35 cm3) was generally smaller than the unaffected side (18.58 ± 2.65 cm3, p < .001). Based on CT, at all ages, the parameters of the unaffected orbit were greater than the affected side. In the 3D scanning and 3D reconstruction based on CT, both unaffected and affected sides were highly correlated. A multiple linear regression equation including three 3D scanning factors was obtained for the orbital volume (R2 = 0.808, p < .001).The retarded orbital volume could be estimated by the parameters based on 3D scanning, along with axial length. In the follow-up stage, 3D scanning can be a novel alternative method to assess the degree of orbital growth retardation in congenital microphthalmia.