Fracture toughness is an important index related to the service safety of marine risers, and weld is an essential component of the steel catenary risers. In this paper, microscopic structure characterization methods such as scanning electron microscopy (SEM) and electron back scatter diffraction (EBSD), as well as mechanical experiments like crack tip opening displacement (CTOD) and nanoindentation, were employed to conduct a detailed study on the influence of the microstructure characteristics of multi-wire submerged arc welded seams of steel catenary riser pipes on CTOD fracture toughness. The influence mechanisms of each microstructure characteristic on fracture toughness were clarified. The results show that the main structure in the weld of the steel catenary riser is acicular ferrite (AF), but there is also often side lath plate ferrite (FSP) and grain boundary ferrite (GBF). With the increase in the proportion of FSP and GBF in the weld microstructure, the CTOD fracture toughness of the weld decreases gradually. The weld AF is a braided cross arrangement structure, and most of the grain boundary orientation difference is higher than 45°. The effective grain size refinement of AF can effectively prevent crack propagation and significantly improve fracture toughness. GBF is distributed along proto-austenitic grain boundaries PAGB, and the large hardness difference between the GBF and the AF matrix weakens the grain boundary. Cracks can easy be initiated at the interface position of the two phases and can propagate along the GBF grain boundary, resulting in the deterioration of toughness. Although the hardness of FSP is between that of GBF and AF, it destroys the continuity of the overall weld microstructure and is also unfavorable to toughness.