Abstract: The sphere-cylinder shell is widely used on ships and ocean engineering, especially in submersible pressure hulls. Submersible floating and sinking process yields alternating stress at the connection part of the sphere and cylinder, causing fatigue damage. However, due to the complexity of the connection around the hatch, the Stress Intensity Factor (SIF) computation of 3D crack at weld toe lacks sufficient research. In this paper, A modeling method based on coordinate transformation is proposed, which can solve the SIF of 3D crack at weld toe of sphere-cylinder combined shells. The accuracy of the proposed method is then verified by calculating surface cracks in pipe and T-shape intersections. Meanwhile, the SIF of surface cracks at hatch weld toe of a 4 500 m manned submersible is also calculated. Furthermore, the method is feasible in calculating SIF of 3D cracks in other types of pressure structures, including cylinders, cones, spheres, or combined ones.