The aim of this study was to confirm On-Board Imager cone-beam computed tomography (CBCT) using the histogram-matching algorithm as a useful method for proton dose calculation.We studied one head and neck phantom, one pelvic phantom, and ten patients with head and neck cancer treated using intensity-modulated radiation therapy (IMRT) and proton beam therapy. We modified Hounsfield unit (HU) values of CBCT and generated two modified CBCTs (mCBCT-RR, mCBCT-DIR) using the histogram-matching algorithm: modified CBCT with rigid registration (mCBCT-RR) and that with deformable image registration (mCBCT-DIR). Rigid and deformable image registration were applied to match the CBCT to planning CT. To evaluate the accuracy of the proton dose calculation, we compared dose differences in the dosimetric parameters (D2% and D98%) for clinical target volume (CTV) and planning target volume (PTV). We also evaluated the accuracy of the dosimetric parameters (Dmean and D2%) for some organs at risk, and compared the proton ranges (PR) between planning CT (reference) and CBCT or mCBCTs, and the gamma passing rates of CBCT and mCBCTs. For patients, the average dose and PR differences of mCBCTs were smaller than those of CBCT. Additionally, the average gamma passing rates of mCBCTs were larger than those of CBCT (e.g., 94.1±3.5% in mCBCT-DIR vs. 87.8±7.4% in CBCT).We evaluated the accuracy of the proton dose calculation in CBCT and mCBCTs for two phantoms and ten patients. Our results showed that HU modification using the histogram-matching algorithm could improve the accuracy of the proton dose calculation.