As the capacity and thermal parameters of turbine generator become larger and higher, the strength design plays increasingly important part in manufacturing process while the traditional strength check method based on the nominal stress which is modified by the stress concentration factor has many disadvantages. The paper proposed Finite Element Analysis (FEA) to analyze the local stress which is more accurate and convenient to seek the dangerous failure point. The possible running conditions which maybe encountered in field are needed to be adequately considered in design process. Two phase short circuit which is the unavoidable condition in the unit’s running porcess plays significant impact on the shafts strength life and the unit’s life-cycle. The paper analyzes the fatigue evaluation of two phase short circuit to enhance the design reasonability as a typical case study. Using FEA and fatigue evaluation methods, more details of the shafts structures and the running processes are taken into accounts which make the dseign process more reliable.