PURPOSE: We evaluated the effect of changing the scan mode of the Elekta X-ray volume imaging cone beam computed tomography (CBCT) on the accuracy of dose calculation, which may be affected by computed tomography (CT) value errors in three dimensions. METHODS: We used the electron density phantom and measured the CT values in three dimensions. CT values were compared with planning computed tomography (pCT) values for various materials. The evaluated scan modes were for head and neck (S-scan), chest (M-scan), and pelvis (L-scan) with various collimators and filter systems. To evaluate the effects of the CT value error of the CBCT on dose error, Monte Carlo calculations of dosimetry were performed using pCT and CBCT images. RESULTS: The L-scan had a CT value error of approximately 800 HU at the isocenter compared with the pCT. Furthermore, inhomogeneity in the longitudinal CT value profile was observed in the bone material. The dose error for ±100 HU difference in CT values for the S-scan and M-scan was within ±2%. The center of the L-scan had a CT error of approximately 800 HU and a dose error of approximately 6%. The dose error of the L-scan occurred in the beam path in the case of both single field and two parallel opposed fields, and the maximum error occurred at the center of the phantom in the case of both the 4-field box and single-arc techniques. CONCLUSIONS: We demonstrated the three-dimensional CT value characteristics of the CBCT by evaluating the CT value error obtained under various imaging conditions. It was found that the L-scan is considerably affected by not having a unique bowtie filter, and the S-scan without the bowtie filter causes CT value errors in the longitudinal direction. Moreover, the CBCT dose errors for the 4-field box and single-arc irradiation techniques converge to the isocenter.