The invention relates to a method for evaluating the water environment disturbance based on characteristic Raman scattering of alga cells, belonging to the technical field of water environment evaluation. The method comprises the following steps: (S1) culturing alga cells under different simulated water environment disturbance factors; (S2) carrying out sampling representation on alga liquid in aculturing period, carrying out Raman imaging on the alga cells by virtue of a confocal microscope Raman spectrometer, and carrying out pretreatment on a Raman spectrum of the alga cells; (S3) analyzing characteristic Raman spectrums of the alga cells under different culturing conditions, so as to obtain the Raman difference of characteristic fingerprints of the alga cells, and determining the category of the alga cells; (S4) establishing a water environment disturbance evaluation model based on the characteristic Raman scattering of the alga cells; and (S5) evaluating and predicting a water environment according to the water environment disturbance evaluation model established in the steps (S4). According to the method, the characteristic Raman spectrum of the alga cells is established andis utilized for predicting the disturbances of different environments, so that the rapid evaluation of the water environment disturbance is realized.