Lutein is the main component of macular and retinal pigment so that it is essential for eye health. In addition, lutein is also related to various metabolic processes in the human body with strong antioxidant properties. The green extraction of lutein in wet microalgae is critical for the further applications as nutraceuticals and pharmaceuticals. Ionic liquid-based aqueous two-phase system (ATPS) is a green approach for multiple product extraction from microalgae. In this study, the extraction performances of ATPS composed of four different cholinium-based compounds (choline geranate, choline chloride, choline dihydrogen citrate and choline bitartrate) and polyethylene glycol 400 (PPG400) were compared. The choline dihydrogen citrate (Ch DHcit) showed a better extraction ability of lutein than other cholinium-based ILs. After optimizing the addition of cholinium-based ILs and PPG400, the ATPS with the best composition (PPG400: Ch Dhcit: water: algal suspension = 42:26:22:10 wt%) was applied to the extraction of lutein from wet Chlorella sp. Six imidazolium-based ionic liquids (1-ethyl-3-methylimidazole chloride, 1-ethyl-3-methylimidazolium bromide, 1-butyl-3-methylimidazolium bromide, 1-butyl-3-methylimidazole chloride, 1-hexyl-3-methylimidazole chloride and 1-hexyl-3-methylimidazolium bromide) were compared as an adjuvant for the lutein extraction from wet Chlorella sp. The introduction of a small amount of 1-ethyl-3-methylimidazole chloride ([C2mim]Cl) improved the extraction efficiency of lutein increased by 9.98 %. In the multiple-times extraction process, the total extraction efficiency of three times distribution reached 102.61 %. This paper provides a new approach to the extraction of lutein from algal biomass.