In order to achieve reliable fatigue crack growth simulations of shafts under cyclic rotary bending by means of the finite element method, the Stress Intensity Factors (SIFs) along a flaw front have to be evaluated for an arbitrary rotational position. However, the evaluation of such SIFs takes much a great computation effort due to geometry modeling necessary to simulate the flaw propagation. In the present study, a fully automated finite element simulation for fatigue growth of flaw, by combining S-FEM, automatic mesh generation technique, and an effective evaluation method of the SIFs, is developed to analyze multi-surface flaw under rotary bending. Fatigue growth simulations of coplanar and non-coplanar parallel surface flaws in shafts under rotary bending are carried out to compare the crack growth behaviors between coplanar and non-coplanar surface flaws.