The invention belongs to the ferment industry, in particular relates to a treatment method of ion exchange waste liquor in lysine production by a fermentation method. The invention adopts a common electrodialysis technology to recycle ammonium sulfate, ammonium chloride or ammonium nitrate in the lysine ion exchange waste liquor produced by extracting the lysine from lysine fermentation production to water solution of ammonium sulfate, ammonium chloride or ammonium nitrate, or adopts a bipolar membrane electrodialysis technology to regenerate sulfuric acid, hydrochloric acid or nitric acid and NH3 by ammonium sulfate, ammonium chloride or ammonium nitrate in the lysine ion exchange waste liquor produced by extracting the lysine from the lysine fermentation production, or adopts the combination of the common electrodialysis technology and the bipolar membrane electrodialysis technology to recycle ammonium sulfate, ammonium chloride or ammonium nitrate in the lysine ion exchange waste liquor produced by extracting the lysine from the lysine fermentation production and regenerate sulfuric acid, hydrochloric acid or nitric acid and NH3. The invention realizes the resource recycling ofthe ion exchange waste liquor and clean production.