A PEG6000/(NH4)2SO4 aqueous two-phase system was chosen as the separation system. The effects of NaCl, Gu(SCN)2 and pH on the partitioning of aloe polysaccharide and bovine serum albumin (BSA) were studied. The result shows that the recovery of aloe polysaccharide was decreased with the increase in pH and the recovery of protein was not changed; NaCl and Gu(SCN)2 can change the partitioning behaviour of the BSA. The separation of BSA and aloe polysaccharides was also carried out. Then, the aloe polysaccharides were obtained by using ultrafiltration membrane. The composition of the polysaccharides was analysed by gas chromatography. The results show that mannose is mainly monosaccharide, and it only contains a few glucose.