This study investigates the influence of shot peening on the fatigue properties of GH4169 alloy at 20 °C, 350 °C and 650 °C in air. Work hardened layer with nanocrystals and deformation twins was generated in GH4169 surface after shot peening. Nanocrystallization process of microstructures was deeply discussed. The effect of twin morphology and compressive residual stress on fatigue properties was then analyzed in detail. Also, the fatigue fracture mechanism was systematically investigated. Results show that the depth of work hardened layer is about 96 μm and the increment of microhardness for the topmost surface reaches approximately 34.6%. Grains are refined to about 9 nm in the topmost surface after shot peening. Original twins are rough...