Structural heterogeneity is generally considered to be an intrinsic feature of metallic glasses (MGs), playing a crucial role in their numerous exceptional properties. Prior studies on the structural and dynamic heterogeneities of MGs mainly focused on multi-element systems, which were possibly caused by chemical variations, challenging to exclude. This study employed a monatomic MG, as an ideal system, to investigate structural heterogeneities despite chemical factors using atomic force microscopy. Our results confirm the persistence of markedly structural heterogeneities in monatomic MGs, which cannot be entirely eliminated through annealing, thereby solidifying the intrinsic nature of structural heterogeneity in amorphous solids. Furthermore, we discover that tuning heterogeneity allows for tailoring the properties of monatomic MGs. This work provides conclusive evidence of the intrinsic property of heterogeneity in amorphous solids, reveals the hidden the complexity which covered by the chemical factors, and could advance the current understanding of the nature of glasses.