The invention discloses a method for separating 2,3-butanediol. The method comprises the following steps: (1) carrying out pretreatment on fermentation broth, so as to obtain clear fermentation broth; (2) adding an inorganic salt and/or an organic acid salt into the clear fermentation broth, carrying out thorough mixing, then, adding a low-polarity organic substance into the clear fermentation broth, carrying out thorough mixing, and then, carrying out standing layering, so as to obtain an upper phase, i.e., a 2,3-butanediol organic solution and a lower phase, i.e., a salt solution; and (3) carrying out electrodialysis desalination treatment on the upper phase, i.e., the 2,3-butanediol organic solution, and collecting a clear solution and concentrated liquor I; and carrying out electrodialysis desalination treatment on the lower phase, i.e., the salt solution by taking the concentrated liquor I as electrodialysis concentrated liquor circulating liquid, collecting and recycling concentrated liquor II, and distilling the clear solution, thereby obtaining the 2,3-butanediol product. According to the method, biomacromolecules such as thallus dissolved protein and lipids can be effectively removed from the fermentation broth so as to form a relatively uniform and pure liquid-phase system, and the implementation of next-step refining manners such as double-aqueous-phase and rectifying is facilitated, so that the method is applicable to large-scale production application.