BackgroundFlatfoot is a condition resulting from complex three-dimensional (3D) morphological changes. Most Previous studies have been constrained by using two-dimensional radiographs and non-weight-bearing conditions. The deformity in flatfoot is associated with the 3D morphology of the bone. These morphological changes affect the force line conduction of the hindfoot/midfoot/forefoot, leading to further morphological alterations. Given that a two-dimensional plane axis overlooks the 3D structural information, it is essential to measure the 3D model of the entire foot in conjunction with the definition under the standing position. This study aims to analyze the morphological changes in flatfoot using 3D measurements from weight-bearing CT (WBCT).MethodIn this retrospective comparative our CT database was searched between 4–2021 and 3–2022. Following inclusion criteria were used: Patients were required to exhibit clinical symptoms suggestive of flatfoot, including painful swelling of the medial plantar area or abnormal gait, corroborated by clinical examination and confirmatory radiological findings on CT or MRI. Healthy participants were required to be free of any foot diseases or conditions affecting lower limb movement. After applying the exclusion criteria (Flatfoot with other foot diseases), CT scans (mean age = 20.9375, SD = 16.1) confirmed eligible for further analysis. The distance, angle in sagittal/transverse/coronal planes, and volume of the two groups were compared on reconstructed 3D models using the t-test. Logistic regression was used to identify flatfoot risk factors, which were then analyzed using receiver operating characteristic curves and nomogram.ResultThe flatfoot group exhibited significantly lower values for calcaneofibular distance (p = 0.001), sagittal and transverse calcaneal inclination angle (p < 0.001), medial column height (p < 0.001), sagittal talonavicular coverage angle (p < 0.001), and sagittal (p < 0.001) and transverse (p = 0.015) Hibb angle. In contrast, the sagittal lateral talocalcaneal angle (p = 0.013), sagittal (p < 0.001) and transverse (p = 0.004) talocalcaneal angle, transverse talonavicular coverage angle (p < 0.001), coronal Hibb angle (p < 0.001), and sagittal (p < 0.001) and transverse (p = 0.001) Meary’s angle were significantly higher in the flatfoot group. The sagittal Hibb angle (B = − 0.379, OR = 0.684) and medial column height (B = − 0.990, OR = 0.372) were identified as significant risk factors for acquiring a flatfoot.ConclusionThe findings validate the 3D spatial position alterations in flatfoot. These include the abduction of the forefoot and prolapse of the first metatarsal proximal, the arch collapsed, subluxation of the talonavicular joint in the midfoot, adduction and valgus of the calcaneus, adduction and plantar ward movement of the talus in the hindfoot, along with the first metatarsal’s abduction and dorsiflexion in the forefoot.