Monte Carlo (MC) simulation of radiation-induced DNA damage involves the usage of many physical/biological parameters, which are often of a large uncertainty. It may hinder the key interpretation of the underlying physical-biological mechanism, yet the quantification process is quite time consuming using the current CPU-based MC packages. Recently, we developed and validated a GPU-based fast microscopic MC simulation tool, goMicroMC. Based on it, we quantified the impacts of DNA single strand breaks (SSBs) and double strand breaks (DSBs) from ten controllable parameters. In goMicroMC, we simulated the physical energy depositions and chemical hydroxyl radicals introduced by the ionizing-radiation via physical, physiochemical and chemical stages. Based on their superpositions with a pre-developed multi-scale nucleus lymphocyte DNA geometrical model, we computed SSBs and DSBs. Both processes were CUDA-GPU-accelerated and validated via comparison to ICRU measurements and Geant4-DNA simulation. As for the parameter tests, we focused on the simulation of mono-energetic electrons (initial kinetic energy of 1/4.5 keV) with a dose deposition of 2 Gy to the cellular nuclear. The ten parameters studied were: 1) physical cross section, 2) electron cut-off energy, 3)-5) three branch-ratios for hydroxyl generations in physicochemical stage, 6) chemical diffusion time, 7)-8) searching radii for direct/indirect damages, 9) energy range for direct damage and 10) probability for indirect damage. We quantified the impacts with “sensitivity” defined as the ratio between the percent change of SSBs/DSBs and that of the parameter. Simulation results from goMicroMC agree with ICRUs and Geant4-DNA within 10% difference. For the parameter tests, taking a sensitivity threshold of 33%, DSBs were especially sensitive to the physical cross section (>1), electron cut-off energy (>0.54) and direct damage radius (>0.5), with both DSBs and SSBs sensitive to the energy range triggering direct damages (>1.1).