We have studied the generation of quasi-periodic (QP) echoes and the associated polarization electric fields by using a fully three-dimensional (3-D) simulation. The 3-D simulation is helpful to investigate realistic structures of the ionospheric plasma. Study of current closure system is one of the important issues and is suitable to be checked by our simulation. We simulated two particular cases: (1) the sporadic- E (Es) layer contains a plasma cloud which has finite zonal elongation and a southward neutral wind applied; and (2) the Es layer has a small sinusoidal perturbation and is at the equilibrium altitude within a rotational wind shear field. In case 1, Hall current driven by the polarization electric field flows within the plasma cloud and turns into the field-aligned current that electromagnetically couples the E-region and the F-region. In case 2, on the other hand, current closure occurs mainly within the Es layer itself. We have found that integrated Pedersen conductivity of the F-region ($Sigma_{P}^{F}$) strongly affects the polarization mechanism in the E-region. In case 2, when the Hall current driven by the polarization electric field can be closed within Es layers, smaller $Sigma_{P}^{F}$ leads to larger polarization electric fields. In case 1, when the Hall current should flow as a field-aligned current to the F-region in order to sustain polarization electric fields, smaller $Sigma_{P}^{F}$ leads to smaller polarization electric fields because $Sigma_{P}^{F}$ serves as a resistance to the Hall current. Mapping of the electric field is also affected by $Sigma_{P}^{F}$. Our results suggest that coupling between the E-region and the F-region is not simply behaved but shows various behaviors depending on the E-region condition.