Nondestructive cryogenically thermal cycling has been a simple but effective treatment to enhance mechanical properties of glassy materials.However,how the structural heterogeneities on nanometer scales are affected by thermal cycling is still an issue.Here,we report the response of spatial hetero-geneities in three selected Ti41Zr25Be28Fe6,Zr56Co14Cu14Al16 and Zr42Y14Co22Al22(at.%)metallic glasses(MGs)with different compositions to the thermal cycling,which show significantly different structure and properties after the same treatments and could be ascribed to the joint contribution of relaxation and rejuvenation induced by thermal cycling.The rejuvenation is initially prevailed in a Zr-Y-containing MG,whereas the relaxation is dominant in a Cu-Co-containing MG,both eventually entering into a dynamic equilibrium state.By employing nanometer-scale structural models,the intrinsic correlation between the spatial heterogeneity and thermal cycling is proposed.The discovery could provide the fundamental understanding of the role of spatial heterogeneity in influencing the macroscopic properties of MGs via thermal cycling and help design high-performance glassy materials by tailoring their atomic structures with suitable thermal treatments.