This study was conducted to estimate the organ equivalent dose and effective imaging dose for four‐dimensional cone‐beam computed tomography (4D‐CBCT) using a Monte Carlo simulation, and to evaluate the excess absolute risk (EAR) of secondary cancer incidence. The EGSnrc/BEAMnrc were used to simulate the on‐board imager (OBI) from the TrueBeam linear accelerator. Specifically, the OBI was modeled based on the percent depth dose and the off‐center ratio was measured using a three‐dimensional (3D) water phantom. For clinical cases, 15 lung and liver cancer patients were simulated using the EGSnrc/DOSXYZnrc. The mean absorbed doses to the lung, stomach, bone marrow, esophagus, liver, thyroid, bone surface, skin, adrenal glands, gallbladder, heart, intestine, kidney, pancreas and spleen, were quantified using a treatment planning system, and the equivalent doses to each organ were calculated. Subsequently, the effective dose was calculated as the weighted sum of the equivalent dose, and the EAR of the secondary cancer incidence was determined for each organ with the use of the biologic effects of ionizing radiation (BEIR) VII model. The effective doses were 3.9 ± 0.5, 15.7 ± 2.0, and 7.3 ± 0.9 mSv, for the lung, and 4.2 ± 0.6, 16.7 ± 2.4, and 7.8 ± 1.1 mSv, for the liver in the respective cases of the 3D‐CBCT (thorax, pelvis) and 4D‐CBCT modes. The lung EARs for males and females were 7.3 and 10.7 cases per million person‐years, whereas the liver EARs were 9.9 and 4.5 cases per million person‐years. The EAR increased with increasing time since radiation exposure. In clinical studies, we should use 4D‐CBCT based on consideration of the effective dose and EAR of secondary cancer incidence.