We investigated the local structure deformation induced by x-ray irradiation in an organic molecular conductor κ-(BEDT-TTF)2Cu[N(CN)2]Br using density-functional-theory (DFT-) based first-principles calculations. Our results demonstrate that the structure change due to x-ray excitation can be predicted by introducing a core hole at specific light atoms of the anion molecules with an infinite lifetime. The formation of a bond-shifted structure triggered by a double excitation was expected as a possible irreversible molecular defect leading to permanent irradiation damage. The calculated change in molecular vibration spectra after irradiation was consistent with the experimental results, and some different vibration modes by further irradiation were also predicted. The calculated local density of states indicates that the bond-shifted structure in the anion layer causes local potential modulation to the carriers (holes) in the cation layer. The introduced potential disorder for the carriers could increase the resistivity due to a localization effect that has been observed experimentally so far.