The laser-induced damage threshold of potassium dihydrogen phosphate (KDP) crystal is far lower than the theoretical value. The damage mechanism of KDP crystal cannot be clearly determined by various experiments and first-principles density functional theory (DFT) calculation of electronic properties. We attempt to explore the impact of phonons on the damage process by studying lattice dynamics. The phonon dispersion curves of intrinsic KDP crystal with harmonic approximation and anharmonic effect are studied by using the first-principles DFT calculations. With harmonic approximation, there are three large imaginary frequencies in the PE phase, which are the O–H stretching soft modes leading to the FE-PE phase transition. For the large displacement vibration of H atoms in PE phase, the room-temperature phonon dispersion curves with anharmonic effect are calculated. The imaginary frequency caused by three O–H stretching soft modes disappears. Our results have important reference significance for understanding the damage mechanism of KDP crystal.