Objective To investigate errors of the force measurement system for clear aligners and to provide suggestion for optimizing the use of this system. Methods The original model was 3D printed and assembled to form the assembly model of the force measurement system. The original and assembly model were named group A and B. Then the assembly model was scanned. GroupA and B model were respectively used to manufacture clear aligners with no activation by thermoforming material respectively. In order to compare whether group A and B models matched well, we carried out overlapping and measured arch width of the two models. Then the force measurement system was used to measure the three-dimensional forces of the teeth received. Student t test was used to compare the differences of measured forces between two groups, which indirectly described the differences between models of the two groups. Results There was an average deviation of -0.126 to 0.188 mm in the models of group A and B after overlapping analysis and measurement of arch width. When the clear aligners made by the original model or assembly model were put on the force measurement system, a certain amount of three-dimensional forces would be measured. The clear aligners made by original model group produced larger forces than that made by the assembly model. Significant differences of the forces between the two groups could be observed in most sites, except the labial & lingual forces of tooth 33 or 32 received, and vertical forces of 32, 31 or 46 received. Conclusions The discrepancy between the original model and the assembly model would affect the measurement of the orthodontic force produced by clear aligners and produce certain systematic errors. In order to reduce the errors generated in the installation procedure, it is necessary to perform a 3D scan of the resin dentition after assembling the force measurement system and to design clear aligners based on the assembly model.