In this study, Scenedesmus sp. FSP3 was cultured using a two-stage culture strategy for CO2 fixation and lutein production. During the first stage, propylene carbonate was added to the medium, with 5% CO2 introduced to promote the rapid growth and CO2 fixation of the microalgae. During the second stage of cultivation, a NaCl concentration of 156 mmol L−1 and a light intensity of 160 μmol m−2 s−1 were used to stimulate the accumulation of lutein in the microalgal cells. By using this culture method, high lutein production and CO2 fixation were simultaneously achieved. The biomass productivity and carbon fixation rate of Scenedesmus sp. FSP3 reached 0.58 g L−1 d−1 and 1.09 g L−1 d−1, with a lutein content and yield as high as 6.45 mg g−1 and 2.30 mg L−1 d−1, respectively. The results reveal a commercially feasible way to integrate microalgal lutein production with CO2 fixation processes.