Microalgae play a vital role in aquatic ecological research, but the fine classification of these tiny and various microalgae cells is still challenging for the community. In this paper, we propose a multimodality technique to simultaneously acquire the polarized light scattering, fluorescence and laser-induced acoustic wave signals originated from individual microalgae cells in water. Experiments of different species of Spirulina and different states of Microcystis have been conducted to test our experiment setup, and the results demonstrate that this method can well discriminate microalgae cells with pigment or microstructural differences. Moreover, with these modalities, the consumption of absorbed energy is evaluated quantitively, and a possible way to assess photosynthesis on a single-cell level is presented. This work is expected to be a powerful technique to probe the biophysical states of microalgae in the aquatic ecosystem.