To explore the influence of cone-beam computed tomography (CBCT) matching reference point selection on target accuracy in intensity-modulated radiotherapy (IMRT) for breast cancer and aimed to provide a reference for clinical application. We conducted a retrospective analysis on breast cancer patients who underwent postoperative radiotherapy between January 2020 and October 2020. CBCT images for image-guided radiotherapy, different matching reference points, and the location of computed tomography (CT) image registration were used to divide patients into the sternum (control group 1), thoracic (control group 2), and sternum-thoracic + target (team) groups. CBCT alignment was confirmed by three different registration methods. After matching, the matching error and spatial displacement of the metal clip at the boundary of the operative cavity in CBCT and target CT were measured and recorded. A total of 528 sets of matching errors and spatial displacement data of metal clips in the target area were obtained for 22 enrolled patients. Independent sample nonparametric tests were used to analyze the significant differences in the three groups of data, and the distance of metal clips in the three groups was calculated. The matching errors of the sternum and study groups were statistically significant, except for the rotation error in the direction of the X-axis (p>0.05). There were no statistically significant differences in the matching error between the thoracic vertebra and the study groups (p>0.05). After the sternum group was matched with the study group, the displacements of the metal clips in the target area of CBCT and CT in the X, Y, and Z directions were as follows: (1.59±1.61) mm and (1.23±1.19) mm (p=0.045), (1.65±1.44) mm and (1.89±1.52) mm (p=0.006), and (1.13±1.18) mm and (1.37±1.31) mm (p=0.999), respectively. The thoracic vertebra group was matched with the study group, and the displacements of the metal clips in the target area of CBCT and CT in the X, Y, and Z directions were as follows: (1.51±1.83) mm and (1.23±1.19) mm (p=0.002), (1.69±1.84) mm and (1.89±1.52) mm (p<0.001), and (0.91±1.28) mm and (1.37±1.31) mm (p=0.003), respectively. Moreover, the 3D vector distances of metal clips in the three groups were (3.16±1.92) mm, (3.62±1.92) mm, and (2.52±1.53) mm, respectively. The selection of optimal reference points for IMRT CBCT automatic registration of breast cancer should simultaneously include the sternum, thoracic vertebra, and target area of the affected side. Placement of a metal silver clip in the intraoperative cavity can improve the matching accuracy of the target area of breast cancer radiotherapy.