The objective of this study was to detective the accuracy of model superimposition and automatic analysis for upper and lower dentition width in Invisalign Progress Assessment during the process of clear aligners. 19 cases were included in this study. Pre-treatment dental cast (T0) and post-treatment dental cast after staged treatment (T1) were available for three-dimensional model superimposition. Subsequently, movements of maxillary teeth in the horizontal plane (cross-section) after staged treatment and width of upper and lower dentition were measured by three-dimensional model superimposition in the real world and Invisalign Progress Assessment separately. Consequently, the data collected from these two methods were compared. In Invisalign Progress Assessment, movements of maxillary teeth in the horizontal plane after staged treatment was 2.31 (1.59,3.22) [median (upper quartile, lower quartile)] millimeter (mm), while in three-dimensional model superimposition, the result was 1.79 (1.21,3.03) mm. The difference between the two groups is significant (P< 0.05). Intercanine width upper, intermolar width upper, intercanine width lower, and intermolar width lower were 36.55 ± 2.76 mm, 56.98 ± 2.62 mm, 28.16 ± 1.85 mm, 53.21 ± 2.72 mm separately in Invisalign Progress Assessment and were 36.48 ± 2.78 mm, 56.89 ± 2.58 mm, 28.05 ± 1.85 mm, 53.16 ± 2.64 mm separately in three-dimensional model analysis, which was no significant difference among these groups (P> 0.05). The data from Invisalign Progress Assessment was not in parallel with what was achieved from model superimposition with palate as a reference completely. The accuracy of model superimposition in Invisalign Progress Assessment needs further investigation, whereas the accuracy of model analysis in Invisalign Progress Assessment was accurate. Thereby, results from Invisalign Progress Assessment should be interpreted with caution by the orthodontist in the clinic.