The relation between the ordering of In ions and the structure variation of homologous compounds InInO3(ZnO)13 and InAlO3(ZnO)m (m = 4, 5, and 13) have been studied by high-resolution transmission electron microscopy. It is revealed that InMO3(ZnO)m is a layered structure, consisting of InO2(1-) (In-O) and MZn(m)Om+1(1+) (M/Zn-O) layers stacked alternatively. Structure variations from the basic one, caused by the ordering of In ions in the M/Zn-O layers, are observed both in In2O3(ZnO)m and InAlO3(ZnO)m. In In2O3(ZnO)m, a modulated structure appearing as zig-zag shaped contrast in the high-resolution image was found and is considered to be caused by the ordering of In ions along the zig-zag contrast area. In InAlO3(ZnO)m, no modulated structure was found. Instead, planar defect structures appearing in Al/Zn-O layers were observed. It is shown that this defect structure is caused by the excess introduction of In ions into the Al/Zn-O layers and the ordering of these In ions. By comparing the results of InInO3(ZnO)m and InAlO3(ZnO)m, it is shown that the reasons for the In ion ordering is the discrepancy between the larger In ion size and the smaller oxygen void for M/Zn ions in M/Zn-O layers.