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 (FE) model of steel bridge decks with initial cracks was established by combining FRANC3D-ABAQUS based on the 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 were analyzed. The results showed that the fatigue cracks in rib-to-deck welded joints details are mixed mode cracks of sequenced Ⅰ-Ⅱ-Ⅲ. 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. The weld penetration rate has marginal 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 increase of the initial crack shape ratio, the crack stress intensity factor decreases.