Laser-induced damage of SiO<sub>2</sub> (α-quartz) is investigated by first-principles calculations. The calculations are based on a coupled theoretical framework of the time-dependent density functional theory and Maxwell equation to describe strongly-nonlinear laser-solid interactions. We simulate irradiation of the bulk SiO<sub>2</sub> with femtosecond laser pulses and compute energy deposition from the laser pulse to electrons as a function of the distance from the surface. We further analyze profiles of laser-induced craters, comparing the transferred energy with the cohesive energy of SiO<sub>2</sub>. The theoretical crater profile well reproduces the experimental features for a relatively weak laser pulse. In contrast, the theoretical result fails to reproduce the measured profiles for a strong laser pulse. This fact indicates a significance of the subsequent atomic motions that take place after the energy transfer ends for the formation of the crater under the strong laser irradiation.