The present invention discloses a method for rapidly quantitating Microcystis aeruginosa in water. The method comprises: preparing a group of Microcystis aeruginosa liquids with different concentrations, determining the absorbance respectively at wavelengths of 220 nm, 360 nm, 420 nm, 520 nm, 640 nm and 680 nm through a spectrophotometer, and counting the algae cells of each sample by using a blood cell plate counting method to obtain the number of the algae cells per unit volume of the algae liquid; determining the absorbance of a blank sample at wavelengths of 220 nm, 360 nm, 420 nm, 520 nm,640 nm and 680 nm, and drawing a calibration curve according to the absorbance and the cell concentration, or obtaining regression equations corresponding to the wavelengths through linear regression; and diluting a Microcystis aeruginosa-containing sample to be measured, determining the absorbance of the algae liquid at the specific wavelengths by using the spectrophotometer, and calculating thecell concentration of the Microcystis aeruginosa in the sample to be measured according to the established calibration curve or regression equation. According to the present invention, with the method, the biomass is determined, such that the important significance is provided for the monitoring and early warning of algal bloom.