The invention relates to a method for treating threonine mother liquor, and concretely relates to the method for treating other waste liquid by using compound enzyme to perform enzymolysis and fermentation of waste thallus and by using a bipolar membrane electrodialysis treatment. According to the invention, the problem of effective components separation on threonine mother liquor, threonine fermentation residual sugar and other components are fully utilized, the method of the invention has the advantages of high energy efficiency, less waste water emission and low pollution; in addition, an electrodialysis technology has the advantages of simple operation, no pollution, long service life and the like, thereby the investment cost of enterprises can be reduced, the energy saving and emission reduction can be carried out, so that the method of the invention serves multiple purposes.