The substructure, fracture morphology and residual stress of shot peened commercial pure titanium were analyzed by the methods of TEM, SEM and XRD. The structure, stress and roughness affecting the fatigue strength were studied in this paper. The results show that twinning plays an important role in plastic deformation of hcp metals, the shot peening layer consists of twins and deformation bands, and the twin interactions can cause micro damage. Fatigue would relax the residual stresses and decrease the strengthening effect. The increased surface roughness has negative effects.