After annealing for various periods of time, the evolution of nanoscale structural heterogeneity and its effect on magnetic properties during structural relaxation are investigated for Fe₈₀Si₉B₁₀Cu₁ amorphous alloy. The nanoscale structural heterogeneity is found to degenerate gradually with relaxation by using the small-angle X-ray scattering and atomic force microscope. Combined with Mössbauer spectroscopy analysis results, the enhanced comprehensive soft magnetic properties of the relaxed alloys can be attributed to the degeneration of nanoscale structural heterogeneity. From the flow unit model, the volume fraction of flow units decreases with relaxation proceeding, and some of the flow units annihilate and transform to the ideal elastic matrix. On the one hand, the relaxed samples with denser packing density have stronger magnetic exchange interaction and higher saturation magnetic flux intensity. On the other hand, the number density of quasi-dislocation dipoles decreases with the annihilation of flow units in the relaxation process, leading to the weakening of the pinning effect of the domain wall. Consequently, the magnetic anisotropy decreases after relaxation, which results in the reduction of coercivity. In this work, the structural mechanism of the evolution of magnetic properties during the relaxation process of Fe₈₀Si₉B₁₀Cu₁ amorphous alloy is investigated from the perspective of structural heterogeneity, which is helpful to establish the correlation between the structure and magnetic properties of Fe-based amorphous alloys.