We employ a unique atomic-resolution high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), often referred to as an atomic-number (Z) contrast method, to investigate the microstructure of a recently developed nanocrystalline Mg alloy with a few addition of Zn and Y. We show that, based on direct imaging of a chemical order, a novel long-period ordered structure is formed in the alloy, which has a unit cell composed of six close-packed planes of the magnesium crystal, with a stacking sequence of ABCBCB' where A and B' layers are significantly enriched by Zn and Y. The present results demonstrate that the additional elements of a few atomic percent to Mg can lead to formation of a long-period chemical-ordered as well as stacking-ordered structure, when the alloy has been synthesized through a non-equilibrium process.