For the first time, nanostructures of 18R (Mg85Zn6Y9) LPSO (long-period stacking-ordered) were examined using STM (scanning tunneling microscopy), which unambiguously confirmed the proposed model of the atomic structure of the LPSO phase in which the Zn–Y clusters are arranged in a two-dimensional hexagonal lattice in the (0001)hcp plane. The typical domain size of this hexagonal arrangement was estimated to range from several nanometers to a few tens of nanometers. In addition, the structures at the domain boundaries of the hexagonal arrangement were imaged and clarified by STM.