Abstract: Aphanizomenon flos-aquae bloom appears regularly nearly at March in recent years. In order to investigate the response of the cyanobacterium A. flos-aquae to the combination of doubled CO2concentration and salinity, an experiment was carried out. Growth rate, photosynthesis, maximal electron transport rate (ETRmax), the ratio of photosynthetic pigment chlorophyll a to phycocyanin (Chl a/ PC) and malondialdehyde (MDA) levels of A. flos-aquae were analyzed. The results demonstrated that salt stress caused decrease in A. flos2aquae growth by disrupting physiological processes, especially photosynthesis. Increased salinity lowered ETRmax. MDA content was increased when salinity elevated. And higher salinity has more distinct effect. Growth rate, ETRmax and Chl a/ PC could be enhanced by elevated CO2concentration, while doubled CO2reduced MDA content.