Ceramic shot were employed to shot-peen the single-crystal superalloy (SX) to analyze the strengthening mechanism of medium-temperature fatigue property. Surface morphology, cross-sectional micro-structure, casting porosities and 650℃ rotating-bending fatigue property were researched, and the fatigue fractures were observed. The results show the 650℃/Kt =1.7 and 650℃/Kt =3 rotating-bending fatigue limit increase by 21.3% and 12.7% after shot peening respectively. Firstly, shot peening eliminated sharp machining masks at the bottom and formed a smooth crater, which reduced the surface stress concentration factor from 1.44 to 1.38. This is the surface topography optimization mechanism. Secondly, a gradient plastic deformation layers were formed at the surface by shot peening, composed of the severe deformation layer at the outer-surface, the deformation layer with the “line structure” at the subsurface, the small deformation layer at the inferior surface and the matrix. The micro-hardness of the deformation layer was 42% higher than that of the matrix, which is the deformation strengthening mechanism. Furthermore, the as-received casting porosities with the diameter 2–10μm, could be the fatigue crack source during alternating stress. The micro-holes closed at the outer-surface and ovalized at the subsurface and inferior surface after at shot peening, which reduced the stress concentration at the casting porosities. The deformation effect on the casting micro-holes of shot peening is the third strengthening mechanism..