To investigate the impact of sagging correction calibration errors in radiotherapy software on image matching. Three software applications were used, with and without a polymethyl methacrylate rod supporting the ball bearings (BB). The calibration error for sagging correction across nine flex maps (FMs) was determined by shifting the BB positions along the Left–Right (LR), Gun–Target (GT), and Up–Down (UD) directions from the reference point. Lucy and pelvic phantom cone-beam computed tomography (CBCT) images underwent auto-matching after modifying each FM. Image deformation was assessed in orthogonal CBCT planes, and the correlations among BB shift magnitude, deformation vector value, and differences in auto-matching were analyzed. The average difference in analysis results among the three softwares for the Winston–Lutz test was within 0.1 mm. The determination coefficients (R2) between the BB shift amount and Lucy phantom matching error in each FM were 0.99, 0.99, and 1.00 in the LR-, GT-, and UD-directions, respectively. The pelvis phantom demonstrated no cross-correlation in the GT direction during auto-matching error evaluation using each FM. The correlation coefficient (r) between the BB shift and the deformation vector value was 0.95 on average for all image planes. Slight differences were observed among software in the evaluation of the Winston–Lutz test. The sagging correction calibration error in the radiotherapy imaging system was caused by an auto-matching error of the phantom and deformation of CBCT images.