The molecular mechanism of blue color formation in an iodine-starch reaction is studied by employing the iodine-alpha-cyclodextrin (alpha-CD) complex as a practical model system that resembles the structural properties of the blue amylose-iodine complex, To this end, we construct, using the quantum chemistry method, a molecular model of the complex (I-5(-)/Li+/2 alpha-CD) that consists of one I-5(-), two molecules of alpha-CD, and a lithium cation, and this model is employed as a basic unit in constructing the structural models of polyiodide ions (I-5(-))(n). The initial structure in the geometry optimization is adopted from the alpha-CD-iodine complex structure obtained from the X-ray crystallography study. The structural models of (I-5(-))(n) are built by adding the basic unit n times along the crystal axis and by optimizing the structure using quantum mechanics/molecular mechanics (QM (iodine)/MM (alpha-CD)) calculations. The electronic absorption spectra of the resulting model structures are calculated by time-dependent density functional theory (TD-DFT). We find that I-5(-) acts as a basic unit of coloration in the visible region. The visible color originates from the electronic transition within the I-5(-) molecule, and any charge transfer between the I-5(-) ion and either of alpha-CD or a coexisting counter cation is not involved. We also reveal that the electronic transitions of (I-5(-))(n) are delocalized, which accounts for the well-known observation that the color of the iodine-starch reaction becomes bluish with an increase in the chain length of amylose. Furthermore, the preresonance Raman spectra calculated from the model suggest that the vibrational motions are localized in the I-5(-) subunit dominantly. A comparison between an experimental absorption spectrum feature of the alpha-CD-iodine complex and the calculated ones of (I-5(-))(n) ions with various n values suggests that (I-5(-))(4) polyiodide ions tend to be populated dominantly in the alpha-CD-iodine complex under aqueous conditions.