Background: The development of personalized and high-precision dental treatment is inseparable from the accurate measurement and analysis of the model. Compared with traditional plaster models, digital models allow dentists to obtain richer and more detailed inspection results. However, the measurement of digital models in clinical practice usually ignores the influence of the overall three-dimensional (3D) structure of teeth and tooth arrangement on the measurement results. The purpose of this study was to evaluate the effect of calibrated tooth axis and tooth arrangement on tooth width and arch length.Methods: A total of 110 digital models from 80 participants were used to measure teeth width and dental arch length using the following methods: Method A, simple positioning of the proximal and distal of teeth; Method B: calibration of the clinical crown axis; and Method C: calibration of the overall 3D axis of the teeth. The Measurand model included pre-and post-orthodontic models of the same patients to assess the impact of tooth alignment on outcomes.Results: In the aligned dentition, whether the tooth axis was calibrated had no effect on the measurement results. On unaligned dentitions, calibrating the pinion allowed for more accurate measurements, with Method C the closest to the true size. Furthermore, the arrangement of teeth affected the measurement, but there was no continuous linear correlation with arch length discrepancy (ALD).Conclusions: Clinicians should choose appropriate measurement methods according to actual needs when performing model measurement, and should pay attention to the influence of tooth axis, tooth shape, and arrangement on the measurement results.