Haematococcus pluvialis is rich in astaxanthin ester (Ast1) and free astaxanthin (Ast2). The astaxanthin is natural antioxidant, and shows higher biodegradability and eco-friendly characteristics than commercial astaxanthin. However, the existing extraction technology is difficult to achieve selectively separation of Ast1 and Ast2. Novel aqueous biphasic systems (ABSs) composed of ionic liquids (ILs) and deep eutectic solvents (DESs) were developed to selectively extract Ast1 and Ast2. The results showed that the ABS composed of tributyloctylphosphine chloride ([P4448]Cl) and choline chloride:d-fructose ([ChCl][Fru]) performed best. The yield and partition coefficient of astaxanthin was 2.35 mg·g−1 and 103.59, respectively. Moreover, Ast1 and Ast2 could be selectively separately with the highest coefficient of specificity of 48.31. Furthermore, the ABS maintained an excellent extraction capacity after three cycles of recycling. As compared with organic solvent extraction and prior methods, the IL-DES ABS is more efficient, recyclable, and environmentally friendly for selectively extraction of astaxanthin.