Due to the wide application of the cone beam computed tomography (CBCT) in clinical practice, it is important to assess radiation dose of CBCT more accurately and efficiently in different clinical applications. This study aims to calculate effective and absorbed doses in CBCT measured in an anthropomorphic phantom using computer-based Monte Carlo (PCXMC) software, and to conduct comparative evaluations of MOSFET (metal- oxide- semiconductor field-effect transistor) and radiophotoluminescence glass dosimeters (RPLGD). Effective and absorbed organ doses are compared with those obtained using MOSFET and RPLGD dosimetry in an anthropomorphic phantom given the same exposure settings. Effective and absorbed organ doses from CBCT during scout and main projections are calculated using PCXMC and PCXMCRotation software, respectively. The mean effective dose from CBCT calculated using PCXMC software is 233.8μSv, while the doses calculated using dosimetry (MOSFET and RPLGD) are 266.67μSv and 268.78μSv, respectively. The X-ray source variation is 0.79%. The prescription limits based on the Friedman test for MOSFET and RPLGD pre-points (i.e., in an analytical analysis of diagnostic names in CBCT) are not statistically significant. The calculated correlation coefficient between MOSFET- and RPLGD-derived absorbed dose values with respect to a field of view CBCT parameter of 17×13.5 mm is r = 0.8623. The study demonstrates that the PCXMC software may be used as an alternative to MOSFET and RPLGD dosimetry for effective and absorbed organ dose estimation in CBCT conducted with a large FOV in an anthropomorphic phantom.