The laser-induced damage threshold (LIDT) of plate laser beam splitter (PLBS) coatings is closely related to the subsurface absorption defects of the substrate. Herein, a two-step deposition temperature method is proposed to understand the effect of substrate subsurface impurity defects on the LIDT of PLBS coatings. Firstly, BK7 substrates are heat-treated at three different temperatures. The surface morphology and subsurface impurity defect distribution of the substrate before and after the heat treatment are compared. Then, a PLBS coating consisting of alternating HfO2–Al2O3 mixture and SiO2 layers is designed to achieve a beam-splitting ratio (transmittance to reflectance, s-polarized light) of approximately 50:50 at 1053 nm and an angle of incidence of 45°, and it is prepared under four different deposition processes. The experimental and simulation results show that the subsurface impurity defects of the substrate migrate to the surface and accumulate on the surface during the heat treatment, and become absorption defect sources or nodule defect seeds in the coating, reducing the LIDT of the coating. The higher the heat treatment temperature, the more evident the migration and accumulation of impurity defects. A lower deposition temperature (at which the coating can be fully oxidized) helps to improve the LIDT of the PLBS coating. When the deposition temperature is 140°C, the LIDT (s-polarized light, wavelength: 1064 nm, pulse width: 9 ns, incident angle: 45°) of the PLBS coating is 26.2 J/cm2, which is approximately 6.7 times that of the PLBS coating deposited at 200°C. We believe that the investigation into the laser damage mechanism of PLBS coatings will help to improve the LIDT of coatings with partial or high transmittance at laser wavelengths.