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 (NPQ f ) was closely related to PPPTM conformational change, as it accounted for as much as 39.42% of the total NPQ. We hypothesize therefore, that NPQ f induced by PPPTM conformation is an important adaptation mechanism for Microcystis blooms under high-intensity light during summer and autumn. In various cyanobacteria, harvested light energy absorbed by phycobilisomes (PBS) is transferred from L CM to the chlorophylls of photosystem II (PSII) and photosystem I (PSI) [1,2]. Some excitons are formed in the reaction center (RC) and are then deactivated through three pathways: photochemical reaction, fluorescence, and thermal dissipation or non-photochemical quenching (NPQ) [3,4]. NPQ is an indispensable pathway of deactivation and plays an important role in protecting PSII from photo-inhibition or photo-damage when exposed to stress conditions [5,6]. Rapid relaxation of NPQ in darkness suggests that algae have a strong vitality and adaptability to high intensity light. NPQ can be deconvoluted into three components based on the different relaxation times in dark periods after exposure to high intensity light [7][8][9]. These three components of NPQ were found to be (i) a fast quenching component (NPQ f ), which refers to the ΔpH-dependent process or high-energy state (qE); (ii) a medium quenching component (NPQ m ), related to the quenching of state transition process (qT); and (iii), a low quenching component (qI), resulting from photo-inhibition of photosynthesis. In cyanobacteria there is no qE dependence on a trans-thylakoid proton gradient [10], although this is the predominant component of NPQ in higher plants [11]. Since