The interaction between structural component flexibility and the closed-loop servo system primarily determines a large reflector antenna pointing system's performance; this is especially true for antennas with a low natural frequency. Because of difficulty and high manufacturing costs of the radome, large antennas usually operate under open-air atmospheres. Therefore, large antennas' pointing performance can be severely influenced by wind disturbances, which can lead to reflector deflection and deformation. Accordingly, this brief has been conducted to determine how to inhibit reflector deflection in order to improve pointing accuracy. Based on a pointing control-oriented model (PCOM) which includes a dynamic model for estimating the servo error and the deformation of the structure caused by wind, this brief proposes a method for overcoming wind disturbance to improve pointing accuracy by evaluating the mode of vibration that influences the most significant beam pointing. First, a dynamic PCOM was established. Second, an antenna pointing controller was designed based on a linear-quadratic-Gaussian approach. Finally, a series of tests and analyses of a 7.3-m Ka-band antenna was conducted; the results show that the maximum pointing error was reduced from 0.0103° to 0.0024° compared with the error experienced with a traditional proportional-integral-derivative controller.