Accurate stress intensity factor analyses and crack growth rate of surface-cracked components in inhomogeneous materials are needed for reliable prediction of their fatigue lift and fracture strengths. This paper describes an automated system for analyzing the stress intensity factors of three-dimensional (3D) cracks in inhomogeneous materials. 3D finite element method (FEM) was used to obtain the stress intensity factor for subsurface cracks and surface cracks existing in inhomogeneous materials. To examine accuracy and efficiency of the present system, the stress intensity factor for a semi-elliptical surface crack in a plate subjected to uniform tension is calculated, and compared with Raju-Newman's solutions. Then the system is applied to analyze cladding effect of subsurface cracks in inhomogeneous materials. The results were compared with those surface cracks in homogeneous materials. It is clearly demonstrated from these analyses that the stress intensity factors for subsurface cracks are less than those of surface cracks.