To optimize the aqueous two-phase extraction and separation technology of flavonoids from citrus peels. The aqueous two-phase systems (ATPS) is PEG/(NH_4)_2SO_4. The effects of amount of added sample, pH value, the mass fraction of PEG 2000 and (NH_4)_2SO_4 on target compounds and phase map of the system were investigated systematically with single factor experiment. In addition, the horizontal interaction of factors on target compounds purification were developed with L_9(3^4) orthogonal experiment. The results showed that PEG with a molecular weight (MW) of 2000, the concentration of PEG 2000 was 25%, the concentration of (NH_4)_2SO_4 was 15%, the concentration of NaCl was 2.0% and the pH was 4 exhibited stronger performance to extract flavonoids for higher hydrophilicity. And pH was the significant influencing factor. And the results of Fourier transform infrared Spectroscop (FTIR) showed that the structural and functional group of the extracts were typical flavonoids. This ATPS of PEG/(NH_4)_2SO_4 system has the advantages of mild conditions, solvent-free residues and less time-consumed, and the obvious efficiency in single-stage separation and purification of flavonoids from citrus peels.