Ice algae have successfully adapted to the extreme environmental conditions in the Antarctic, however the underlying mechanisms involved in the regulation and response of thylakoid membranes and chloroplast to low-temperature stress are still not well understood. In this study, changes in pigment concentrations, lipids, fatty acids and pigment protein complexes in thylakoid membranes and chloroplast after exposure to low temperature conditions were investigated using the Antarctic ice algae Chlamydomonas sp. ICE-L. Results showed that the chloroplasts of Chlamydomonas sp. ICE-L are distributed throughout the cell except in the nuclear region in the form of thylakoid lamellas which exists in the gap between organelles and the starch granules. Also, the structure of mitochondria has no obvious change after cold stress. Concentrations of Chl a, Chl b, monogalactosyl diacylglycerol, digalactosyl diacylglycerol and fatty acids were also observed to exhibit changes with temperature, suggesting possible adaptations to cold environments. The light harvesting complex, lutein and β-carotene played an important role for adaptation of ICE-L, and increasing of monogalactosyl diacylglycerol and digalactosyl diacylglycerol improved the overall degree of unsaturation of thylakoid membranes, thereby maintaining liquidity of thylakoid membranes. The pigments, lipids, fatty acids and pigment-protein complexes maintained the stability of the thylakoid membranes and the normal physiological function of Chlamydomonas sp. ICE-L.