To evaluate the impact of deformation magnitude and image modality on deformable-image-registration (DIR) accuracy using Halcyon megavoltage cone beam CT images (MVCBCT).Planning CT images of an anthropomorphic Head phantom were aligned rigidly with MVCBCT and re-sampled to achieve the same resolution, denoted as pCT. MVCBCT was warped with twenty simulated pre-known virtual deformation fields (T, i = 1-20) with increasing deformation magnitudes, yielding warped CBCT (wCBCT). The pCT and MVCBCT were registered to wCBCT respectively (Multi-modality and Uni-modality DIR), generating deformation vector fields V and V' (i = 1-20). V and V' were compared with T respectively to assess the DIR accuracy geometrically. In addition, V, T, and V' were applied to pCT, generating deformed CT (dCT), ground-truth CT (G) and deformed CT' (dCT') respectively. The Hounsfield Unit (HU) on these virtual CT images were also compared.The mean errors of vector displacement increased with the deformation magnitude. For deformation magnitudes between 2.82 mm and 7.71 mm, the errors of uni-modality DIR were 1.16 mm ~ 1.73 mm smaller than that of multi-modality (p = 0.0001, Wilcoxon signed rank test). DIR could reduce the maximum signed and absolute HU deviations from 70.8 HU to 11.4 HU and 208 HU to 46.2 HU respectively.As deformation magnitude increases, DIR accuracy continues to deteriorate and uni-modality DIR consistently outperformed multi-modality DIR. DIR-based adaptive radiotherapy utilizing the noisy MVCBCT images is only conditionally applicable with caution.