The microstructure and stress/strain evolution laws of TC21 titanium alloy pulsed laser-MIG welded joints under composite waveform and variable amplitude fatigue (CWVAF) were investigated, and the twinning evolution and phase transformation mechanism were revealed. Under an applied initial maximum cyclic stress \({\sigma}_{1}\) of 350 MPa, the evolution from dislocations and stacking faults to twins was observed in α′ phase. During this process, the uneven cyclic plastic deformation of two intersecting α′ phases with different angles resulted in the nucleation of twins in the α′ phase with severe deformation. With the increase in \({\sigma}_{1}\) , the number and size of twins were gradually increased. The interrupted tests and molecular dynamics simulations indicate that during the CWVAF process, the phase transformation from β phase to α phase occurred initially in the regions with lower Cr content within the β phase (grain boundary). As the \({\sigma}_{1}\) increased, the phase transformation was gradually extended toward the interior of β phase. Under σ1 = 350 MPa, the low stress level led to a small driving force for phase transformation, allowing the transformed α phase to grow slowly and undergo coordinated deformation. However, under σ1 = 410 MPa, the growth of the transformed α phase was inhibited. Meanwhile, the dislocations piled up at the interfaces until the initiation and propagation of cracks occurred. Additionally, at σ1 = 350 MPa, the combined effect of phase transformation and twinning induced two obvious strain releases at 31 and 62 pct of the fatigue life. In contrast, under the higher stress of σ1 = 410 MPa, only one strain release was induced by phase transformation at 44 pct of the fatigue life.