Abstract: The natural red pigment and pectin in pitaya peel were separated simultaneously by aqueous two-phase system(ATPS)to promote the development of pitaya peel resource. Taking pitaya peel as raw material,the extraction of red pigment and pectin from pitaya peel by PEG/(NH₄)₂SO₄ ATPS was studied. Four different factors followed as PEG relative molecular weight,weight fraction of PEG,system pH,weight fraction of ammonia sulfate were investigated based on the extraction yield of red pigment and pectin from pitaya peel. The results showed that the extraction yield of pigment and pectin increased with the increasing of the weight fraction of PEG and ammonia sulfate. When the phase ratio was close to 0.5,the pigment in the upper phase and pectin in the lower phase showed better separation. The optimum conditions for ATPS was pH4.0 using ATPS of PEG6000 and ammonia sulfate,with the weight fraction of 16% and 19%,respectively. Under these conditions,the extraction yield of the desired red pigment enriched in the upper phase of ATPS was 1.82%±0.04%,while the pectin was enriched in the lower phase of ATPS with an extraction rate of 3.68%±0.13%. In conclusion,the ATPS could simultaneously separate pigment and pectin from pitaya peel,with the advantages of mild operational conditions,simple process and high yield. The study was supposed to provide the experimental basis for the comprehensive utilization and development of pitaya peel.