Despite numerous studies on β relaxation of amorphous alloys, the relationship between structural heterogeneity and β relaxation and the effect on magnetic properties of Fe-based amorphous alloys is still unknow. In this work, the structure and magnetic properties of Fe84-xZr6B10Mx (M = Si, Cu; x = 0, 0.6, 1 at%) amorphous alloys were investigated. With the increase of Si content, the negative value of average chemical affinity (∆Hchem) of the alloys is increased, leading to the synergetic enhancement in structural heterogeneity and β relaxation. In addition to this, the increase of liquid-like regions (LLRs) reduces saturation magnetic flux density (Bs) and increases coercivity (Hc). However, the addition of Cu element decreases the negative value of ∆Hchem of the alloys, resulting in weakening of structural heterogeneity and β relaxation synergetically. The reduction of LLRs has resulted in increase in Bs. Moreover, Fe-Cu atom pairs with positive enthalpy of mixing increases the local density of quasi dislocation dipoles (QDDs), resulting in the increase of Hc.