Saponin chemical composition was phenotyped and genotyped, and saponin composition-based geographical genetic diversity and differentiation were evaluated in Chinese wild soybean (Glycine soja Sieb. & Zucc.). Thirty-two phenotypes and 34 genotypes were confirmed from 3805 wild soybean accessions. Eleven phenotypes (Aaα_K, Aaα_IK, Aaα_IJK, AaBcEα_J, AaBcα_K, AbEα_IJ, Abα_K, Abα_IK, Abα_IJK, Abβ_HAb and Aβ₀) were newly detected. Four genes had frequencies: Sg-1^a 78.8% and Sg-1^b 21.0% at the Sg-1 locus; Sg-4 30.7% and Sg-6e 13.7% at their respective loci. The north-eastern and southern populations showed high genetic diversity; the Northeast region contained more novel variants (AuAe, A0, A0Bc, α_H, α_I α_J, α_K, and Abβ_HAb), and the southern populations contained high frequencies of the Sg-4 gene. Gene differentiation (F_st) analysis suggested that Sg-4 and four group-α saponin alleles or genes (Sg-6e, Sg-6h, Sg-6i, Sg-6j) were important factors influencing the genetic structure and differentiation in Chinese wild soybeans. Geographical differentiation was characterised mainly by latitudinal differences, with two primary groups (north and south) based on saponin genes. Chinese wild soybean accessions differed from Japanese and South Korean ones in genetic structure based on saponin composition, the latter two being likely to have spread from southern China in the glacial stages during the last Ice Age.