The invention relates to the field of microalgae identification, and in particular relates to a method for rapid identification of microalgae on a single cell level based on a single cell Raman spectrum. The method comprises the following steps: collecting single cell Raman spectrums of microalgae cells, establishing a microalgae single cell Raman spectrum database, and comparing a single cell Raman spectrum of unknown microalgae with the established microalgae single cell Raman spectrum database, thus realizing microalgae identification or mutant screening on the single cell level. The method disclosed by the invention identifies the microalgae through a single cell Raman spectrum technology; a simple, rapid and non-invasive microalgae identification method on the single cell level is provided, thus providing an efficient discrimination method for microalgae identification and mutant screening.