The geoelectric fields induced by late-time high altitude electromagnetic pulse (HEMP E3) and geomagnetic storms lead to low frequency geomagnetically induced currents in the transmission grids, and the resulting half-cycle saturation of a large number of transformers could potentially threaten the power system voltage stability. However, in the existing study on HEMP E3 effect evaluation, it typically assumes a uniform or 1D layered earth structure, without adequately considering the influence of lateral variations in earth conductivity on the induced geoelectric fields. Thus, it is difficult to rigorously assess the electromagnetic security of power systems under complex geological conditions such as coasts. This paper establishes a 3D computational model for HEMP E3 geoelectric fields based on finite element method, then studies the influence of complex earth conductivity structure on the spatiotemporal distribution of HEMP E3 geoelectric fields, and finally evaluates the power system voltage stability via electromagnetic transient simulation method. The results uncover substantial changes in the amplitude and duration of HEMP E3 geoelectric fields near the conductivity interface, which may lead to significant deviation in the voltage stability results of the power system. The method developed in this paper provides an important basis for the HEMP effect evaluation and protection of infrastructure located in complex geological areas.