The additional local stress concentration caused by undercut and misaligned defects could lead to lower fatigue strength of welded joints. The paper aims to investigate the effects of undercuts and misalignments on fatigue performance and reliability of Load‐carrying Cruciform Welded Joint (LCWJ) quantitatively by probabilistic statistics theory and fracture mechanics theory. Firstly, the geometrical characteristics of undercut and misalignment are summarized from the literature and our experiments. Subsequently, the probabilistic distributions of material fracture properties, the configurations of geometries, and flaws were evaluated under specific loading conditions. The fatigue strengths are further estimated by the probabilistic reliability theory by combining the actual fatigue data. The results demonstrate a clear disparity of fatigue crack growth threshold and resistances for the tested data of base metal and weldment. The level of defects determines the interval of fatigue life, and the larger the dispersion accompanying earlier fatigue failure occurs.