The studies on absorption spectra of Y-doped ZnO have presented two distinctly different experimental results, which are the red shift and blue shift on the optical bandgap and absorption spectra when the mole fraction of impurity increases from 0.0313 to 0.0625. To solve this contradiction, the calculations in this paper are carried out by the CASTEP tool in the materials studio software based on the first-principal calculations of norm conserving pseudopotential of the density functional theory, and the geometric structures of ZnO, Zn0.9687Y0.0313O, Zn0.9583Y0.0417O and Zn0.9375Y0.0625O systems are constructed. By using the method of GGA+U, we calculate the band structure, density of state, electron density difference, population, orbital charges and absorption spectrum. The results show that with the doping amount increasing from 0.0313 to 0.0625, both the lattice parameters and the volume of doping system increase: the higher the total energy of the doping system the higher the formation energy of the doping system is, thereby making doping difficult and the stability of the doping system lower Increasing Y-doping concentration weakens the covalent bond, strengthens the ionic bond; as Y doping concentration increases, the Mulliken bond populations and bond lengths of Y-O parallel and vertical to c-axis decrease for the doping system. Meanwhile, the more the Y doping content, the wider the optical bandgap of the doping system becomes and thus more significant the blue shift of absorption spectra of Y-doped ZnO systems will be. The calculation results of absorption spectra of Y-doped ZnO system are consistent with the experimental data. And the contradiction between blue shift and red shift of absorption spectra of Y-doped ZnO system is explained reasonably. These results may contribute to the improvement of the design and the preparation of short wavelength optical devices from Y-doped ZnO.