To solve the problem of beam pointing jitter in laser applications, a laser beam pointing stability optimization scheme based on Gaussian process regression was proposed. The composition and principle of the laser beam pointing stability system device were introduced, and the principle of Gaussian process regression method and its advantages as the fast stabilization control algorithm for laser beams were discussed. After optimization by this method, the pointing jitter reaches 2.3 μrad in the horizontal direction and 3.3 μrad in the vertical direction, which improves the pointing stability of the laser system by more than an order of magnitude. The pointing jitter is 20% of the existing linear feedback system, and has a significant effect on high-frequency noise optimization. This study is of great significance for precision experiments and precision machining that are sensitive to the directionality of laser beams.