During the industrial magnesium production, the thermal balance in a magnesium electrolysis cell is the key factor for regular operations. If the thermal balance is broken, the efficiency of the regular production declines seriously because of too high or too low of a temperature in the magnesium cell. The thermal balance in the magnesium cell is determined directly by the thermal field, which is based on the electric field energy. The thermoelectric field in the magnesium cell must be studied by coupling for the high correlation between the two fields. A three-dimensional half of a full cell model was developed through the finite element analysis software to coupling study the thermoelectric field in a 120 kA magnesium electrolysis cell. Through numerical calculation, the distribution of the voltage and temperature were obtained. Moreover, the total heat generation and dissipation in the cell are influenced by the changes of the current intensity because the electric field is the source of the thermal field. When the current intensity changed, the thermal balance may be broken. To investigate the effects on the fluctuation of the current intensity that occurred in the practical production, the thermal balance in the magnesium cell was studied by changing the current intensity from 115 to 125 kA. With the changes of the current intensity, the corresponding electrolyte depth must be carried out to maintain the thermal balance. From the simulation results, the electrolyte depth has a linear relation with the current intensity on the basis of the thermal balance in the cell and the method is an efficient way to maintain the thermal balance in the cell.