The changes of the substructure, the residual stress and the surface roughness of shot peened pure titanium were analyzed by means of SEM, TEM, XRD and surface roughness measurements in this paper. The results show that shot peening increased the fatigue strength of pure titanium. The substructures of shot peened pure titanium consist of dislocations, deformation twins and deformation bands. Fatigue loading will relax the compressive residual stress and decrease the strengthening effect. The increased surface roughness has negative effects.