In this paper is given a three-dimensional numerical simulation of the eddy current welding of rails where the longitudinal two directions are not ignored. In fact, usually it is considered a model where, in the two-dimensional numerical simulation of rail heat treatment, the longitudinal directions are ignored for the magnetic induction strength and temperature, and only the axial calculation is performed. Therefore, we propose the electromagnetic-thermal coupled three-dimensional model of eddy current welding. The induced eddy current heat is obtained by adding the z-axis spatial angle to the two-dimensional electromagnetic-thermal, thus obtaining some new results by coupling the numerical simulation and computations of the electric field and magnetic induction intensity of the three-dimensional model. Moreover, we have considered the objective function into a weak formulation. The three-dimensional model is then meshed by the finite element method. The electromagnetic-thermal coupling has been numerically computed, and the parametric dependence to the eddy current heating process has been fully studied. Through the numerical simulation with different current densities, frequencies, and distances, the most suitable heat treatment process of U75V rail is obtained.