During the welding process of the aero-engine magazine, the weld will directly affect the fatigue performance and service life of the whole magazine as a weak part. The post-weld heat treatment is normally used to eliminate the welding thermal stress, uniform the structure of weld joint and improve the performance, however the improvement effect on fatigue life is insufficient. This paper innovatively proposes the electromagnetic coupling treatment technology to regulate the heat treated Ti2AlNb electron beam welds to improve the fatigue life of welded joints and at the same time investigates the evolution of the material structure in the weld joints after electromagnetic coupling treatment. The results showed that the fatigue limit of the weld joint was increased from 134.2 MPa to 159.4 MPa, an improvement of 18.8%. After the electromagnetic coupling treatment, the residual compressive stress was increased by up to 128.7%. Meanwhile, without changing the material organization and phase composition, dislocation walls and dislocation entanglement are generated within the material without changing the microstructure and phase composition, and the fatigue crack source is moved from the surface to the subsurface, thus reducing fatigue crack expansion rate, resulting in the improvement of fatigue performance. The coupling effect of Joule heat effect, electron wind effect and magnetoplastic effect promotes the dislocation movement and enhances the fatigue crack expansion. This study provides a new method to enhance the fatigue life of welds and provides a feasibility basis for electromagnetic coupling treatment to enhance the fatigue performance of welds.