Cone-beam computed tomography (CBCT) is an important tool for patient positioning in radiotherapy due to its outstanding advantages. However, the CBCT registration shows errors due to the limitations of the automatic registration algorithm and the nonuniqueness of manual verification results. The purpose of this study was to verify the feasibility of using the Sphere-Mask Optical Positioning System (S-M_OPS) to improve the registration stability of CBCT through clinical trials. From November 2021 to February 2022, 28 patients who received intensity-modulated radiotherapy and site verification with CBCT were included in this study. S-M_OPS was used as an independent third-party system to supervise the CBCT registration result in real time. The supervision error was calculated based on the CBCT registration result and using the S-M_OPS registration result as the standard. For the head and neck, patients with a supervision error ≥3 or ≤-3 mm in 1 direction were selected. For the thorax, abdomen, pelvis, or other body parts, patients with a supervision error ≥5 or ≤-5 mm in 1 direction were selected. Then, re-registration was performed for all patients (selected and unselected). The registration errors of CBCT and S-M_OPS were calculated based on the re-registration results as the standard. For selected patients with large supervision errors, CBCT registration errors (mean ± standard deviation) in the latitudinal (LAT; left/right), vertical (VRT; superior/inferior), and longitudinal (LNG; anterior/posterior) directions were 0.90±3.20, -1.70±0.98, and 7.30±2.14 mm, respectively. The S-M_OPS registration errors were 0.40±0.14, 0.32±0.66, and 0.24±1.12 mm in the LAT, VRT, and LNG directions, respectively. For all patients, CBCT registration errors in the LAT, VRT, and LNG directions were 0.39±2.69, -0.82±1.47, and 2.39±2.93 mm, respectively. The S-M_OPS registration errors were -0.25±1.33, 0.55±1.27, and 0.36±1.34 mm for all patients in the LAT, VRT, and LNG directions, respectively. This study shows that S-M_OPS registration offers comparable accuracy to CBCT for daily registration. S-M_OPS, as an independent third-party tool, can prevent large errors in CBCT registration, thereby improving the accuracy and stability of CBCT registration.