In this study, ultrasound was applied to control membrane fouling development online in an anaerobic membrane bioreactor (AMBR). Experimental results showed that membrane fouling could be controlled effectively by ultrasound although membrane damage may occur under some operational conditions. Based upon the observation on the damaged membrane surface via SEM, two mechanisms causing membrane damage by exerting ultrasound are inferred as micro particle collide on the membrane surface and chemical interaction between membrane materials and hydroxyl radicals produced by acoustic cavitations. Not only membrane damage but also membrane fouling control and membrane fouling cleaning were resulted from these mechanisms. Properly selecting ultrasonic intensity and working time, and keeping a certain thickness of cake layer on membrane surface could be effective ways to protect membrane against damage.