To investigate errors of force measurement system for clear Aligners and provide references for optimizing the use of this system. Methods The original model was three-dimensional (3D) printed and assembled to form the assembly model of the force measurement system, then the assembly model was scanned. The original model (Group A) and the assembly model (Group B) were used to manufacture clear Aligners with no activation by thermoforming material respectively. Overlapping analysis and measurement of arch width were performed on Group A and B models, so as to compare whether two groups of models matched well. The force measurement system was used to measure the 3D force of the resin teeth after the clear Aligners were put on, and the differences of dental force between two groups were analyzed. Results The results of overlapping analysis and measurement of arch width showed that there was an average deviation of -0.126 mm to 0.188 mm in Group A and B models. When the clear Aligners made by the original model or assembly model were put on the force measurement system, a certain amount of 3D forces would be measured. The clear Aligners made by the original model produced larger forces than that made by the assembly model. Significant differences of the forces between two groups could be observed in most sites after the clear Aligners were put on, except the labial & lingual forces of tooth 33 or 32, and vertical forces of tooth 32, 31 or 46. Conclusions The discrepancy between the original model and the assembly model will cause certain systematic errors. In order to reduce the errors generated in installation procedure, it is necessary to perform 3D scanning of the resin dentition after assembling the force measurement system, and to design clear Aligners based on the assembly model.