With the continuous development of manufacturing technology of micro/nano devices based on GaN, focused gallium ion beam has become a momentous method for machining complex GaN structures. Therefore, this study focuses on the characterization and simulation of sputtering etched profile by Ga FIB on GaN substrate. First, the profile characterization experiments are carried out to analyze the influence of ion dose, dwelling time, and scan area, and the results reflect that the sputtering etched regularity on GaN substrate differs from that on Si substrate, especially in redeposition effect, milling rate, and droplet phenomenon. In addition, the forming mechanism of droplet phenomenon is discussed, and the milling experiments are conducted to research the droplets avoidance method, which shows that the appearance of droplets is impacted by ion dose and dwelling time. Finally, the sputtering yield of GaN under focused gallium ion beam is measured and sorted, and the simulation program is developed based on continuous cellular automaton (CCA) model. This work can provide a guidance for the further application of GaN-based materials.