Emergent phenomena and functions arising from topological electron-spin textures in real space or momentum space are attracting growing interest for new concept of states of matter as well as for possible applications to spintronics 1-5 . One such example is a magnetic skyrmion 3-5 , a topologically stable nanoscale spin vortex structure characterized by a topological index. Real-space regular arrays of skyrmions are described by combination of multi-directional spin helixes. Nanoscale configurations and characteristics of the two-dimensional skyrmion hexagonal-lattice have been revealed extensively by real-space observations 6-8 . Other three-dimensional forms of skyrmion lattices, such as a cubic-lattice of skyrmions, are also anticipated to exist 9,10 , yet their direct observations remain elusive. Here we report real-space observations of spin configurations of the skyrmion cubic-lattice in MnGe with a very short period (~3 nm) and hence endowed with the largest skyrmion number density. The skyrmion lattices parallel to the {100} atomic lattices are directly observed using Lorentz transmission electron microscopes (Lorentz TEMs). It enables the first simultaneous observation of magnetic skyrmions and underlying atomic-lattice fringes. These results indicate the emergence of skyrmion-antiskyrmion lattice in MnGe, which is a source of emergent electromagnetic responses 9,11 and will open a possibility of controlling few-nanometer scale skyrmion lattices through atomic lattice modulations.The discovery of giant magnetoresistance 12,13 in magnetic multilayers opened a new field, i.e., spintronics, of controlling motions of electrons using structures of spin ensemble 14 . In solids, spins interact with electron orbits at specific atomic sites. This spin-orbit (or spin-orbital) interaction is the origin of emergent states and phenomena,