Despite the mesoscopic isotropic nature of metallic glasses, there is a certain degree of structural heterogeneity down to the nanoscale. However, how structural heterogeneity affects the magnetic properties is still unclear. In this work, the relaxation-induced structural heterogeneity and magnetic properties evolution of Fe80Si9B11 metallic glass were investigated by atomic force microscopy (AFM) and Mössbauer spectroscopy. We revealed that the correlation-length of nanoscale heterogeneity relates closely with the ferromagnetic exchange interaction together with the magnetic anisotropy, providing experimental evidence of the intrinsic link between the nanoscale structural heterogeneity and magnetic properties for Fe-based metallic glasses. The degeneration of nanoscale structural heterogeneity induces the enhancement of the ferromagnetic exchange interaction and weakening of the magnetic anisotropy. Our results have a vital significance in understanding the structure-property relationship of metallic glass.