A comparative study was conducted to determine the structural hot-spot stress at the weld toe of the welded joint in the orthotropic steel bridge deck by use of different methods. The finite element models of the welded joint were established by the finite element software ANSYS with the solid element and the shell element, respectively. Seven types of the mesh size were divided adjacent to the weld toe zone. The structural hot-spot stress at the weld toe of the welded joint in the orthotropic steel bridge deck was calculated using the direct extraction method, the surface extrapolation method, and the structural stress method. The results obtained from different methods were compared in respect of the accuracy and the sensitivity with the mesh size and the element type. The achieved results reveal that when the finite element models are constructed by use of different mesh sizes and element types, the structural hot-spot stress calculated by the direct extraction method and the surface extrapolation method has significant discreteness, while the structural hot-spot stress derived from the structural stress method has good consistency.