First, Monascus pigments were transferred from nonionic surfactant micelle aqueous solution into ionic liquid phase by ionic liquid based microemulsion extraction, in which the recovery yield of yellow Monascus pigments based on absorbance at 410 nm reached to 95.5%. Then, the yellow Monascus pigments in the ionic liquid phase were recovered by ionic liquid–butanol two-phase extraction, in which the recovery yield of yellow Monascus pigments reached to approximately 95%.