The ability of algae to produce lipids comprising of unsaturated fatty acids varies with strains and culture conditions. This study investigates the effect of temperature on the production of unsaturated fatty acids in Scenedesmus sp. grown on oil crop residue based medium. At low temperature (10 degrees C), synthesis of lipids compromising of high contents of unsaturated fatty acids took place primarily in the early stage while protein accumulation mainly occurred in the late stage. This stepwise lipid-protein synthesis process was found to be associated with the contents of acetyl-CoA and alpha-KG in the algal cells. A mechanism was proposed and tested through simulation experiments which quantified the carbon flux allocation in algal cells at different cultivation stages. It is concluded that low culture temperature such as 10 degrees C is suitable for the production of lipids comprising of unsaturated fatty acids.