A high non-photochemical quenching (NPQ) appeared below the phase transition temperature when Microcystis aeruginosa PCC7806 cells were exposed to saturated light for a short time. This suggested that a component of NPQ, independent from state transition or photo-inhibition, had been generated in the PSII complex; this was a fast component responding to high intensity light. Glutaraldehyde (GA), commonly used to stabilize membrane protein conformations, resulted in more energy transfer to PSII reaction centers, affecting the energy absorption and dissipation process rather than the transfer process of phycobilisome (PBS). In comparison experiments with and without GA, the rapid light curves (RLCs) and fluorescence induction dynamics of the fast phase showed that excess excitation energy was dissipated by conformational change in the photosynthetic pigment proteins on the thylakoid membrane (PPPTM). Based on deconvolution of NPQ relaxation kinetics, we concluded that the fast quenching component (NPQf) was closely related to PPPTM conformational change, as it accounted for as much as 39.42% of the total NPQ. We hypothesize therefore, that NPQf induced by PPPTM conformation is an important adaptation mechanism for Microcystis blooms under high-intensity light during summer and autumn.