The invention relates to a method for synchronously enhancing yields of lutein and carbohydrates of autotrophic microalgae. The method comprises the following steps: inoculating alga seeds into a seed culture medium, culturing to obtain a seed solution, inoculating the seed solution into a photobiological reactor filled with a fermentation culture medium, and culturing. In the culturing process, the initial illumination intensity is controlled at 60-300 mu mol/m<2>/s, and the illumination intensity is enhanced by 50-150 mu mol/m<2>/s every 12 hours until the fermentation finishes; and meanwhile, when the initial nitrogen source concentration starts exhaustion, a nitrogen source with the nitrogen concentration of 2-14 g/L is fed at the constant speed of 1-10 mg/L/h, and the fermentation period is 4-6 days. The biomass concentration of the microalgae cultured by the method can reach 4-9 g/L, the yield of lutein is 20-60 mg/L, and the yield of carbohydrates is 1.4-3.3 g/L. The method has the advantages of short fermentation period, simple production technique and low production cost, and can obviously widen the industrialization prospects for simultaneously producing lutein and biofuels by using microalgae.