The effect of dose-delivery time with flattening filter (FF) and flattening filter-free (FFF) photon beams based on microdosimetric kinetic model (MKM) was investigated in this study. Monte Carlo simulation with the particle and heavy ion transport code system (PHITS) was performed to calculate the dose-mean lineal energy yD (keV/μm) of FF and FFF 6 MV photon beams using the IAEA phase-space files of Varian TrueBeam linear accelerator. Human non-small cell lung cancer NCI-H460 cells were used to determine the MKM parameters under the condition that dose-delivery times with continuous irradiation were 1, 5, 10, 30, and 60 min, and the adsorbed dose was 2, 4, and 8 Gy in this study. In addition, the relative biological effectiveness (RBE) of FF and FFF photon beams were calculated for evaluating the effect of dose delivery time. The RBE of FF decreased to 99.8% and 97.5% with 5 and 60 min for 2 Gy in comparison to 99.6% and 95.1% for 8 Gy, respectively. Meanwhile, that of FFF decreased to 99.5% and 94.9% with 5 and 60 min for 2 Gy in comparison to 99.5% and 94.9% for 8 Gy, respectively. Dose-delivery time has an effect on the RBE with photon beams. In other words, the dose-delivery time should be considered during radiation therapy. Furthermore, FFF photon beams were an effective irradiation method compared to FF in dose-delivery time on account of improving clinic throughput.