Abstract: To study the effects of ultrasound wave on the blue-green algae (Microcystis aeruginosa), blue-green algae were exposed to ultrasound waves (40W) for 20 minutes, and then cultured for 1, 3, and 5 days. The results indicated that the biomass of suspended algae cells reduced by 97.84% at Day 3. From Day 1 to Day 3, lipid bodies and cyanophycin granules were accumulated, and thylakoid layers were cracked, and phycobilisomes attached to thylakoid dropped off in the cells. At Day 5, the nucleoid area gradually shrinked or disappeared, the cell infrastructure disintegrated, and voids appeared in cytoplasm and intracellular granules were degraded. Moreover, the photosynthetic oxygen evolution rate decreased by 24.83% on Day 3. Chl.a content reduced by 23.75% on Day 5. SOD activity and CAT activity were induced by ultrasound, although both of the activities diminished from Day1 to Day 5. The amount of intracellular organic exudation increased after treatment. The activities of three ATPases (Na+/K+-ATPase, Mg2+-ATPase and Ca2+-ATPase) increased firstly and then decreased, which was related to the change of membrane permeability. These results suggested that ultrasound wave may reduce algae photosynthesis, damage photosynthetic pigments and increase the membrane permeability, which can cause oxidative damage and induce death of M. aeruginosa. The dynamic CAT and ATPases activities suggested that M. aeruginosa may enhance antioxidant enzymes activity as well as ion regulation and energy activity to resist the ultrasound stress, and that the growth and metabolism of algae cells began to recover over time while the enzyme activities began to decline.