The Mn-Si alloy system undergoes the ͑-Mn→ ␣-Mn+ R͒ eutectoid reaction at 908 K around 8 at. % Si. The crystal structures of the -Mn, ␣-Mn, and R phases were reported to consist of complex coordination polyhedra such as a polyhedron with coordination number ͑CN͒ 12: that is, an icosahedral atomic cluster. The notable features of these structures are that both the ␣-Mn and R structures are characterized by arrays of penetrated CN16 pairs while penetrated CN14 pairs are present in the -Mn structure. In a penetrated CN16 pair consisting of two CN16 polyhedra, for instance, a center atom of one CN16 polyhedron is one of 16 atoms forming a shell of the other. To understand the crucial factors controlling a change between two coordinationpolyhedra structures, in this study, the crystallographic features of the ͑-Mn→ ␣-Mn͒ and ͑-Mn→ R͒ structural changes related to the eutectoid reaction have been investigated by transmission electron microscopy. It was found that the former ͑-Mn→ ␣-Mn͒ change started with the conversion of a penetrated CN14 pair into a penetrated CN16 pair by successive and simple atomic shifts. Among three types of orientation relations between the -Mn and R structures in the latter change, the direct conversion of a penetrated CN16 pair from a penetrated CN14 pair should first occur for the major relation. As for two other minor relations found mainly for higher Si contents, in the starting changes, a penetrated pair consisting of CN14 and CN12 polyhedra, and two neighboring CN14 and CN12 polyhedra in the -Mn structure must be converted to a penetrated CN16 pair, and two neighboring CN16 and CN12 polyhedra in the R structure, respectively. The directional relation in the orientation relationship for these two structural changes was, as a result, determined by orientations of the penetrated CN14 pairs or two neighboring polyhedra in the -Mn structure. It is thus understood that the crucial factor controlling the ͑-Mn→ ␣-Mn͒ and ͑-Mn→ R͒ structural changes should be the conversion between the structural units consisting of only two neighboring polyhedra, which are involved in these complex structures. Furthermore, both site occupancies of atoms and atomic-bond lengths in the penetrated CN16 pairs for the ␣-Mn and R structures were evaluated to understand the physical origin of interplay between the appearance of a magnetic moment in the former structure and the formation of covalentlike atomic bonding in the latter.