The invention provides a lysine preparation method and application thereof and relates to the technical field of biochemical engineering. The lysine preparation method comprises providing and inoculating suspended bacterial colonies of lysine producing bacterial strains into a mixed fermentation medium for fermentation to obtain a fermentation liquor mixture, performing solid-liquid separation onthe fermentation liquor mixture to obtain fermentation liquor, and performing extraction and purification on the fermentation liquor. By performing fermentation with the suspended colonies of the lysine producing bacterial strains, which can be suspended in the fermentation medium and in full contact with nutrient solution in the fermentation medium, the efficiency of lysine production can be greatly improved; meanwhile, the lysine preparation method applies bean husks and bean dregs as the raw materials of the fermentation medium, so that agricultural product processing waste residues can beeffectively utilized on the one hand, and on the other hand, the rich lysine composition substances in the bean husks and the bean dregs can be conveniently utilized by the lysine producing strains toproduce lysine, and further the yield of lysine can be greatly increased.