The construction of new renewable energy infrastructures and the development of new ocean resources continues to proceed apace. In this regard, the increasing size and capacity of offshore wind turbines demands that the size of their accompanying supporting marine structures likewise increase. The types of marine structures utilized for these offshore applications include gravity base, monopile, jacket, and tripod structures. Of these four types, monopile structures are widely used, given that they are comparatively easy to construct and more economical than other structures. However, constant exposure to harsh cyclic environmental loads can cause material deterioration or the initiation of fatigue cracks, which can then lead to catastrophic failures. In this paper, a 3D fatigue finite element analysis was performed to predict both the fatigue life and the crack initiation of a welded monopile substructure. The whole analysis was undertaken in three steps. First, a 3D non-steady heat conduction analysis was used to calculate the thermal history. Second, a thermal load was induced, as an input in 3D elastoplastic analysis, in order to determine welding residual stresses and welding deformation. Finally, the plastic strain and residual stress were used as inputs in a 3D fatigue FE analysis in order to calculate fatigue crack initiation and fatigue life. The 3D fatigue finite element analysis was based on continuum damage mechanics (CDM) and elastoplastic constitutive equations. The results obtained from the 3D fatigue finite element analysis were compared with hot spot stresses and Det Norske Veritas (DNV-GL) standards.