The crystal structures of the two types of iodine complexes (complex I and II) of poly(vinyl alcohol) (PVA), which were prepared respectively from the KI/I-2 aqueous solution of middle (0.1-0.5 mol/L) and high (1-3 mol/L) concentration of I-2, have been analyzed quantitatively on the basis of 2-dimensional X-ray diffraction diagrams and Raman spectral data in addition to the computer simulation method. In the crystal lattice of the original PVA, the PVA chains of zigzag conformation are packed together by intermolecular hydrogen bonds. Once the I-3(-) ions migrate into the crystal lattice of PVA, these hydrogen bonds are deconstructed and the PVA chains are displaced from the original positions so that the I-3(-) ions can be coupled together with the PVA chains through the charge-transfer between the I-3(-) and hydroxyl groups, resulting in the formation of complex I. In this complex, the averaged occupancy of I-3(-) ions is about 0.2, and the PVA-iodine pairs and the original PVA chain pairs coexist to form a kind of super lattice with the disordered packing structure of PVA chains and iodine ion columns. As the iodine concentration is increased furthermore, most of the PVA chains are combined with I-3(-) ions at the occupancy of about 0.7 to create the complex II. The comparison of X-ray end diffraction patterns of the doubly oriented samples clarified the spatial relation of the crystal lattices between PVA, complex I and complex II. In the original PVA sample, the planar-zigzag planes of PVA chains are parallel to the rolled plane of the doubly oriented sample. This geometrical relation is kept in the complex I sample. However, in the complex II, the PVA chains have been found to rotate by 38 degrees around the chain axis in the transition process from complex I to complex II. In this way, the change in the packing mode of PVA chains and iodine ions in the complex formation process has been successfully revealed for the first time from the atomic level.