We developed a novel dosimetric method using DNA molecules as a radiation sensor. The amount of neutron or gamma rays irradiated DNA damage was determined by evaluating the amount of DNA serving as a template for qPCR. The absorbed doses in the samples were estimated using the tally of the “t-product” in the data from the PHITS Monte Carlo particle transport simulation code. The neutron fluence for each sample was measured using the niobium activation reaction ⁹³Nb (n, 2n) ^92mNb, and the absorbed dose per neutron fluence was estimated to be 7.1 × 10⁻¹¹ Gy/(n/cm²). Based on the PHITS modeling, the effects of neutron beams are attributed to the combination of proton and alpha particle beams. The results from qPCR showed that neutrons caused more DNA damage than gamma rays. The qPCR method demonstrated that neutron irradiation caused 1.13-fold more DNA damage compared to gamma ray irradiation; however, this result did not show a statistically significant difference. This method we developed, using DNA molecules as a radiation sensor, may be useful for biodosimetry.