Four different weld shapes were obtained by choosing appropriate electron beam welding parameters, which are respectively named as bell shape, funnel shape, nail shape, and wedge shape. Fatigue examinations of the electron beam welded joints with different shapes were carried through. The influence of weld shape on fatigue performance of the joints was synthetically evaluated by analytic hierarchy mathematical model. The results show that weld shape effects fatigue property of the joint by electron beam welding. The sequencing of fatigue performance of the joints with four different shapes by analytic hierarchy process is bell shape, funnel shape, wedge shape, and nail shape. It is validated by practical trial results that the analytic hierarchy mathematical model is effective and practical.