The motile cells lost their flagellae and became palmella cells with thickened cell walls. Our previous study showed that motile and palmella cells are both capable of coping with environmental stress to different extents; however, the development of the protective mechanisms during encystment was not well understood. This study combined several physiological and biochemical tools to investigate several key photosynthetic and subcellular biochemical changes during the encystment. The chlorophyll fluorometric analysis demonstrated that the capacity to dissipate excessive NSC-718781 excited energy via the NPQ mechanism developed during encystment and was further augmented when palmella cells were subjected to HL. NPQ is a rapid and effective process that is induced seconds after photosynthetic cells are exposed to excess light. When the excited energy exceeds the capacity of algal cells to use the reducing energy produced by photosynthesis for carbon fixation, algal cells can lower the quantum yield at PSII by dissipating the excess absorbed energy by NPQ. Thus, the development of NPQ in palmella cells may reduce the production of excessive ROS under HL conditions. The adjustment of relative numbers of PSII and PSI complexes represents an important mechanism by which plants and algae prevent photodamage during high-light acclimation. PSI cyclic electron transport may have multiple functions in photoprotection, such as dissipating energy absorbed at PSI and maintaining a DpH for NPQ to down-regulate energy production at PSII. H. pluvialis cells changed the energy balance between PSII and PSI under HL by enhancing the quantum yield of PSI while reducing Y.We speculate that increasing the PSI/PSII ratio, decoupling PSI and PSII by decreasing cytochrome b6f during encystment, and increasing cyclic electron transport around PSI are a suite of photoprotective mechanisms developed in palmella cells for acclimation under HL. This study revealed for the first time the global remodeling of H. pluvialis glycerolipids in response to HL and under encystment. The ability of living cells to survive under extreme environmental conditions may rely on their ability to modify their membrane composition and adjust their lipid desaturation level. Prominent TAG accumulation, coupled with a reduction in the number of chloroplast lipid molecules species, was observed in palmella cells. TAG biosynthesis requires considerable amounts of reducing equivalents, which may help relax overreduced photosynthetic electron transport chains and thus protect the cells under stress. In addition, TAG constitutes the storage subcellular structure for synthesized astaxanthin molecules in H. pluvialis, which can in turn provide protection from excess light. TAG may also be a depot of polyunsaturated fatty acids in some microalgae, allowing the organisms to swiftly adapt to the changing environment; the polyunsaturated fatty acids can be reincorporated into membrane lipids.