Objective: This study investigated the dependences of mucosal dose and photon energy distribution on the flattened and unflattened photon beams using Monte Carlo simulation. Methods: A heterogeneous mucosa phantom with a variation of mucosal thickness (0.5–3 mm) was irradiated by the 6 and 10 MV flattened and unflattened photon beams generated by a Varian TrueBeam linac. The photon energy distributions at the mucosa and depth doses at the bones and mucosa were calculated using the EGSnrc-based Monte Carlo code. Results: It is found that the 6 MV unflattened photon beam contained more particle fluence in the low-energy range (0–100 keV) than the 10 MV. However, mucosal doses for the unflattened photon beams were found lower than the flattened. This is different from the skin dose having dose enhancement on the unflattened beam compared to the flattened, though both mucosal and skin structure involve an air-soft tissue interface. The particle fluence of the 6 and 10 MV unflattened photon beams increased with an increase of the mucosal thickness. This agreed well with the relative depth doses that increased in the ranges of 3.4%–3.6% and 2.5%–3.0% at the upper mucosa, and 5.1%–5.7% and 2.9%–3.2% at the lower mucosa, with their thickness increasing from 0.5–3 mm for the 6 and 10 MV unflattened photon beams. Conclusion: It is concluded that the unflattened photon beam results in a lower mucosal dose than the flattened, and the 6 MV unflattened beam has a larger dependence of mucosal dose on its thickness when compared to the 10 MV.