Abstract: A three-dimensional cloud model with detailed hail-bin microphysics coupled with the electrification process is developed to simulate electric charges and discharging processes in a severe thunderstorm in Beijing. The results indicate that the charge transfer between cloud droplets and graupel, and the spatial distribution of charge density are primarily influenced by cloud water through inductive charging mechanism. However, influnces on the distribution of charge density from the liquid water content including rain water are mainly through influcencing the polarity and quantity of transfered charges between graupel and snow (or ice) crystals in the non-inductive charging processes for different liquid water contents. Different cloud microphysical processes may produce an inhomogeneous distribution of the source and sink of hydrometeors, which causes the inhomogeneous distribution of hydrometeors on different vertical cross sections and leads to the complicated charge separation due to both inductive and non-inductive charging processes. At the same time, the charge transfer due to mass transfer of hydrometeors is not homogeneous. Ice phase hydrometeors are carried to higher altitudes by strong updraft, and therefore, lead to charges transfer occurring at higher altitudes. There are several centers of snow particles at the top and flanks of strong updraft. The graupel particles distribution is relatively homogeneous, but the content centers incline towards the lee side of updraft. Therefore, non-inductive charging process mainly occurs on the leeward side of updraft where the divergent airflow occurs, which causes the total charges to distribute primarily in this area. Due to strong updraft, several content centers of ice phase hydrometeors form in different areas, and this lead to that one type of hydrometeor may carry different charge polarity (or quantity) in different areas, especially at the mature stage of the severe thunderstorm, so that the multi-layer charge structure develops easily. Due to the changes of electrical charge structure by the discharge process, the induced charges at lightning channels redistribute on the surface of each hydrometeor category, and this process may complicate the charge transfer induced by the mass transfer of hydrometeors during the interaction between microphysical and dynamical processes. Further research on the effect of lightning on electric charge structure is needed. In all, the factors mentioned above play important roles in producing the multi-layer distribution of electric charges.