The invention relates to an asymmetric synthesis method of (S, S)-2,8-diazabicyclo[4,3,0]nonane, using N-benzyl-butenedimide as raw material, and N-p-toluenesulfonyl-N`-propeniminohydrazine (Ⅱ) in the presence of chiral square amide catalyst (Ⅲ) through asymmetric [2+4] addition reaction to obtain 8-benzyl-2-p-toluene Sulfonamido-7,9-dioxo-(1S,6R)-2,8-diazabicyclo[4,3,0]-3-ene nonane, followed by recrystallization, reduction, acid-catalyzed hydrolysis, The reduction step affords (S,S)‑2,8‑diazabicyclo[4,3,0]nonane. The synthesis method of the invention is simple, the yield of the asymmetric catalytic product is high, the enantioselectivity of the product after recrystallization can be as high as 90%, the condition is mild, the operation is simple, the production cost is low, and it can be used in industrialized production.