Abstract: In this paper irradiation simulations on a voxel model of HaCaT cell were performed using Geant4 and ROOT for low energy α particle, and the process of the secondary electron produced by α particle was depicted. Aiming at speciality about cell structure, the characteristic values about microdosimetry were investigated by several situations, which include seven kinds of energy of α particle, four kinds of source distributions and eight kinds of source-target combinations. The track structure of low energy α particle, radial space distribution and energy spectra distribution of secondary electron, single-event specific energy distribution and S value of sub-cell were all acquired. The change characteristics and influence rule of microdosimetry in sub-cell for α particle were analyzed, and quantitative description of microdosimetry for virtual cell in sub-cellular scale was realized.