Double-sided welding is expected to improve the fatigue resistance of rib-to-deck welded joints, and the initial welding defect is the key factor affecting the fatigue performance of these joints. A multi-scale finite element model of steel bridge decks with initial cracks was established by using FRANC3D-ABAQUS technology based on fracture mechanics theory. The stress intensity factor of fatigue crack in the rib-to-deck welded joints was studied. The influences of weld penetration rate, thickness of deck plate and initial crack shape ratio on the stress intensity factor of fatigue crack of double-sided welded joints were analyzed. The results showed that the fatigue cracks in rib-to-deck welded joints details are mixed mode cracks of I-II-III, led by mode I. The maximum stress intensity factor of fatigue crack of rib-to-deck double-sided welded root was 64.3% lower than that of single-sided weld, which can effectively improve the fatigue performance of rib-to-deck welded joints. The weld penetration rate has little effect on the stress intensity factor of fatigue crack in the rib-to-deck double-sided welded joints. Thickening the deck can effectively reduce the stress intensity factor of the fatigue crack in the rib-to-deck double-sided welded joints. With the increase of the initial crack shape ratio, the crack stress intensity factor decreases.