A large number of titanium alloy structural components in aircraft are joined and assembled through holes. The complex service conditions pose high requirements for the fatigue performance of the holes. The study aims to use expansion deformation to induced gradient nanostructures and residual stress enhance the fatigue performance of Ti6Al4V holes. By studying the evolution process of the microstructure in titanium alloys, the formation mechanism of gradient nanostructures has been obtained, and their impact on various stages of fatigue fracture is analyzed. The results showed that the split sleeve cold expansion (CE) process caused severe plastic deformation on the surface of the hole, resulting in a large amount of LAB production and a transformation of the main texture components. Meanwhile, the gradient nanostructures are formed on the hole surface, which include nanocrystalline layer, superfine lath grain layer, lath grain layer and severe deformation layer. During the expansion deformation process, the slip of dislocations leads to the formation of high-density dislocation structures, which evolve into subgrain boundaries and then undergo dynamic recrystallization through subgrain rotation to achieve grain refinement. What's more, the degree of grain refinement, depth of gradient nanostructure, and residual stress increase as the expansion deformation intensifies. The depth of gradient nanostructure is 300 μm, and the maximum residual stress is −419 MPa, when the deformation is 5 %. The combined effect of gradient nanostructures and high residual compressive stress induced by expansion deformation has increased the total fatigue life and crack propagation life of CE-5 specimen by 2.9 and 3.4 times compared to NCE specimen. This work provides an effective method and theoretical analysis for improving the fatigue life of titanium alloy holes.