An aqueous two-phase system (ATPS) consisting of acetone and phosphate was used to extract acetoin from fermentation broth. The influence of phase composition on partition of acetoin was investigated. When the filtered fermentation broth was used, relatively high partition coefficient (22.3) and recovery coefficient (96.4%) of acetoin were obtained by a system composed of 30% (w/w) acetone and 35% (w/w) dipotassium hydrogen phosphate. Then the system was applied to extract unfiltered fermentation broth directly, and the recovery coefficient of acetoin was 94.3%. Simultaneously, the byproduct 2,3-butanediol could also be extracted with the recovery coefficient of 93.5%. In addition, the removal of residual sucrose, cells, proteins, and prodigiosin from the fermentation broth was studied, and the removal ratios of these impurities were all above 85%. Ultimately, the recovery of phosphate in the bottom phase was explored, and the recovery coefficient could reach 93.7% through pH adjustment and dilution crystallization. The recovered phosphate also showed good ATPS extraction ability. This method provides a new possible way for the separation of acetoin from fermentation broth.