Production of red Monascus pigments can be enhanced by extractive fermentation in a nonionic surfactant micelle aqueous solution. Using excess MSG (monosodium glutamate) as the sole nitrogen source, several kinds of red Monascus pigments, including red Monascus pigments with MSG residue as major components, were produced during the fermentation process. However, the corresponding downstream processing, i.e., isolation of red Monascus pigments from the nonionic surfactant aqueous solution, remains unsolved. In the present work, a novel ionic liquid-nonionic surfactant aqueous two-phase system, such as coacervate phase: ionic liquid ([Bmim]Cl) = 1:3 (W/W) and temperature = 60 degrees C, was developed for transferring of the anionic red Monascus pigments with MSG residue from nonionic surfactant micelle aqueous solution into ionic liquid aqueous solution. Thus, the challenging isolation of red Monascus pigments from nonionic surfactant aqueous solution was converted to the relatively easy separation between red Monascus pigments and water-miscible ionic liquid. By screening various organic solvents, water-chloroform two-phase system was selected for recovery of red Monascus pigments from the water-miscible ionic liquid. Finally, the isolated red Monascus pigment with MSG residue was confirmed by UPLC MS analysis.