The laser-induced damage threshold of optical elements is a key indicator for measuring laser damage resistance. Optical elements with periodic surfaces have advantageous optical characteristics and potential applications in high-power laser systems. It is important to determine the laser-induced damage threshold accurately. In this paper, the main sources of uncertainty are analyzed, a calculation formula for the uncertainty of laser-induced damage threshold is established, and the processing methods for reducing the uncertainty of laser-induced damage threshold are provided. The results show that when the spot radius is 400 μm, the error is 10 μm, the laser energy error is 5%, and the uncertainty introduced by energy density is zero. Then, the main factors contributing to the uncertainty of the laser damage threshold are the uncertainty of the damage probability and that of the linear fitting. The precision of the laser-induced damage threshold can be further improved by increasing the number of measurements for each energy level.