The Steel Catenary Riser (SCR) is a vital component for transporting oil and gas from the seabed to the floating platform. The harsh environmental conditions and complex platform motion make the SCR's girth-weld prone to fatigue failure. The structural stress fatigue theory and Master S-N curve method provide accurate predictions for the fatigue damage on the welded joints, which demonstrate significant potential and compatibility in multi-axial and random fatigue evaluation. Here, we propose a new frequency fatigue model subjected to welded joints of SCR under multi-axial stress, which fully integrates the mesh-insensitive structural stress and frequency domain random process and transforms the conventional welding fatigue technique of SCR into a spectrum analysis technique utilizing structural stress. Besides, a full-scale FE model of SCR with welds is established to obtain the modal structural stress of the girth weld and the frequency response function (FRF) of modal coordinate, and a biaxial fatigue evaluation about the girth weld of the SCR can be achieved by taking the effects of multi-load correlation and pipe-soil interaction into account. The research results indicate that the frequency-domain fatigue results are aligned with the time-domain results, meeting the fatigue evaluation requirements of the SCR.