Blooms　of　cyanobacteria　cause　ecological　imbalance,　killing　a　large　number　of　water　plants,　fish　and　other　aquatic　organisms.　In　addition　to　easily　cause　algae　toxin　emission,　the　traditional　processing　method　has　drawbacks　of　short　period　of　time　and　high　energy　consumption.　Ultrasonic　technology,　as　the　environmental　and　effective　method,　is　put　forward　to　control　the　algae　biomass.　However,　most　studies　based　on　inhibitory　effect　of　ultrasound　irradiation　on　algae　were　conducted　at　the　algae　photosynthesis　system,　the　physiological　activity　of　other　indicators　was　not　in-depth　studied,　and　most　of　which　were　the　short-term　effects　with　unknown　timeliness.　The　objective　of　this　paper　was　to　explore　the　suitable　ultrasonic　parameters　to　remove　algae　and　the　influence　of　ultrasonic　frequency　and　power　on　physiological　activity　both　from　physiological　activity　and　biomass　control　of　algae　cells.　The　results　showed　that　the　physiological　and　metabolic　activities　of　algae　were　lower　and　the　number　of　intact　cells　decreased　after　ultrasonic　radiation.　The　proportion　of　damaged　cells　was　proportional　to　the　ultrasonic　power　density.　DNA　fragments　were　not　detected　after　ultrasonic　irradiation　and　DNA　chain　structure　remained　complete.　The　effects　of　ultrasonic　parameters　on　algae　density　were　also　studied.　When　the　power　density　was　0.02　W/mL,　the　effect　of　treatment　under　ultrasonic　frequency　of　40　kHz　was　better　than　that　of　20　kHz　and　100　kHz.　It　is　suggested　to　use　ultrasonic　treatment　with　the　frequency　of　40　kHz　and　power　density　of　0.0245　W/mL　to　treat　the　blue-green　algae.　©　2017　Desalination　Publications.　All　rights　reserved.