Effects of shot peening on high cycle fatigue limitation of the powder metallurgical nickle-based FGH4097 superalloy at room temperature were investigated in this article. Fatigue fracture characteristics and shot peening surface morphology were observed by SEM, the sample surface residual stresses σ_r and microhardness H were determined by X-ray diffraction stress tester and ultra-small dynamic microhardness tester, and EBSD and TEM were used to observe the microscopic characteristics of the shot peening layer. The results show that compressive residual stresses induced by shot peening are more deeper and more stable than without shot peening, which is beneficial to improve the resistance of fatigue crack initiation and reduce crack propagation rate. And the high dislocation density, a large number of low-angle boundary and a small number of soft orientation grain in the surface layer of shot peening make the fatigue crack difficult to initiate at the surface. So, 20.7% increasing at high cycle fatigue limitation of the FGH4097 superalloy at room temperature.