Marine algae are diverse photosynthetic organisms, profoundly rich in bioactive compounds. Temperature is a major factor in algal cultivation and biomass production. At the cellular level, the change of temperature is reflected in oscillating algal lipid/fatty acid profile and inhibition of photosynthetic activities. The function of thylakoid membrane system is intimately dependent on its lipid matrix, however the molecular organization of these lipid membranes and particularly their adaptive arrangements under temperature stress remain largely unexplored. The present work employing extensive atomistic simulations provides the first atomistic view of the phase transition and domain coexistence in model membrane composed of thylakoid lipids of a marine alga, between 10-40 °C. The model membrane undergoes a transition from a gel-like phase at 10-15 °C to a homogeneous liquid-disordered phase at 40 °C. Clear evidences of spontaneous phase separation into coexisting nanoscale domains are detected at intermediate temperatures. Particularly at 25-30 °C, we identified the formation of a stable rippled phase, where the gel-like domains rich in saturated and nearly hexagonally packed lipids separated from fluid-like domains enriched in lipids containing polyunsaturated chains. Cholesterol impairs the phase transition and the emergence of domains, and induces a fairly uniform liquid-ordered phase in the membrane over the temperatures studied. The results have implications in understanding the role of lipids in temperature adaptation in algal.