The paper discusses radiation dose of dual energy CT on which copper modulation layer, is mounted in order to improve diagnostic performance of the dual energy CT. The radiation dose is estimated using MCNPX and its results are compared with that of the conventional dual energy CT system. CT X-ray spectra of 80 and 120 kVp, which are usually used for thorax, abdominal, head, and neck CT scans, were generated by the SPEC78 code and were used for the source specification ‘SDEF' card for MCNPX dose modeling. The copper modulation layer was located 20 cm away from a source covering half of the X-ray window. The radiation dose was measured as changing its thickness from 0.5 to 2.0 mm at intervals of 0.5 mm. Since the MCNPX tally provides only normalized values to a single particle, the dose conversion coefficients of F6 tally for the modulation layer-based dual energy CBCT should be calculated for matching the modeling results into the actual dose. The dose conversion coefficient is 7.2*10⁴ cGy/output that is obtained from dose calibration curve between F6 tally and experimental results in which GAFCHORMIC EBT3 films were exposed by an already known source. Consequently, the dose of the modulation layer-based dual energy cone beam CT is 33∼40% less than that of the single energy CT system. On the basis of the results, it is considered that scattered dose produced by the copper modulation layer is very small. It shows that the modulation layer-based dual energy CBCT system can effectively reduce radiation dose, which is the major disadvantage of established dual energy CT.