The results of a modeling study of the variations of altitude ion density distribution in the nighttime E region over the magnetic equator during strong magnetospheric substorms and storms due to perturbations of the zonal electric field Ey are presented. The ion density N is calculated by solving the time-dependent continuity equation for ion density by assuming the time variations of Ey, which are fitted to some of the observed ones. It is shown that during severe magnetospheric disturbances, the altitude structure of the nighttime equatorial E region is substantially modified, with the largest effects in the lower part of E region (z < 105 km), where a deep trough in ion density is formed instead of the quiet E region maximum. The ion density in the trough can be ~1/6 times the undisturbed value of N. The E region maximum NmE can be lifted up by ~30 km, being ~2¿ decreased as compared with the quiet time value of NmE. In the course of the magnetospheric disturbance the E region is bifurcated into two layers.