Flue gas desulfurization (FGD) wastewater treatment is currently of interest, as stringent standards have been released in order to limit the pollution emissions from the energy industry, and concerns about water scarcity are also increasing. Reverse osmosis (RO) membrane is a promising alternative for highly efficient FGD wastewater treatment. However, membrane fouling strongly limits its application. This study developed a suitable treatment system by combining RO membrane with ultrasonic cleaning. The introduction of low-frequency and high-intensity ultrasonic cleaning improved the cleaning efficiency of membrane fouling, as the permeate flux recovered 49% of the reduced value within 10 min of cleaning. The lifespan of the membrane was also extended, as the time of permeate flux declined to the same level, increasing from 2 h to 4 h after ultrasonic cleaning. The effluent of the system could meet the standard of desulfurization wastewater treatment. The treatment system is feasible for FGD wastewater treatment at a laboratory scale. These findings proved that the combination of RO membrane and ultrasonic cleaning could be applied to FGD wastewater treatment. The study provided an efficient, cost-saving, and convenient way to develop the FGD wastewater treatment system.