Taking the typical algae of Microcystis aeruginosa and Scenedesmus obliquus in reservoirs as study objects, the self-developed photobioreactor was used to study the effects of light fluctuation on the growth status and photosynthesis of algae. The experiment results showed that the biomass of the Microcystis aeruginosa decreased by 14%, the color was slightly yellow, while the biomass of the Scenedesmus obliquus was reduced by 24% and seriously yellowed when under fluctuating light than under static light intensity of 6100 lx; The chlorophyll-a and carotenoid of Microcystis aeruginosa decreased 12.7% and 55.5%, respectively, which of Scenedesmus obliquus decreased 78% and 74%, respectively; The photosynthetic parameters Fv/Fm, YⅡ and ETR of the two algae decreased and the heat flux NPQ increased, and the photosynthesis was inhibited and the growth and metabolism were weakened, which provided a theoretical basis for the control of algae by the internal wave.