A geomagnetic storm is a periodic natural disaster in which the changing geomagnetic field can induce an induced geoelectric field. A geomagnetic induced current (GIC) loop is formed between the transmission line and the earth conductor through the neutral points of grounding transformers. GIC seriously threatens the safe and stable operation of extra-high and ultra-high voltage AC transmission systems. There are many types of terrain and complex structures in our country, which makes the influence of geological landforms on induced geoelectric fields very significant. This paper proposes a finite element calculation method for GIC based on a three-dimensional earth conductivity model to address the difficulties in modeling and calculating GIC. Firstly, a three-dimensional earth conductivity model is established considering the anisotropy of geological structures. Meanwhile, a calculation model for electromagnetic field penetration depth under multi-layer geological conditions is given. Secondly, a mathematical model based on time-varying electromagnetic fields is established. Combined with the topology of the power grid, an equivalent calculation model for the power grid GIC is derived. Finally, taking the Shache-Turpan 750 kV transmission line in Xinjiang province as an example, a corresponding physical model is built in COMSOL Multiphysics finite element simulation software. The three-dimensional distribution of the induced ground electric field in the power grid is obtained through geometric modeling, boundary condition setting, grid division, and iterative solution. Furthermore, the GIC flowing through the neutral point of the 750 kV transformer is obtained. The research results indicate that the overall level of GIC obtained by the 3D model is higher than that of the 2D model. Besides, the 3D model considers the geometric angle between the transmission line and different terrains, which can provide a more detailed distribution of induced geoelectric fields. The research results verify the effectiveness of the method proposed in this paper, which provides a reference basis for scientific planning of ultra-high and ultra-high voltage transmission corridors.