Notoginsenoside R2 is a crucial active saponin in Panax notoginseng (Burk.) F. H. Chen, but its natural content is relatively low. In this study, we investigated the biotransformation of notoginsenoside R1 to 20(S/R)-notoginsenoside R2 using Lactiplantibacillus plantarum S165, compared the inhibitory effects on cancer cell proliferation and conducted a mechanistic study. Notoginsenoside R1 was transformed using Lactiplantibacillus plantarum S165 at 37 °C for 21 days. The fermentation products were identified using a combination of HPLC, UPLC-MS/MS, and ¹³C-NMR methods. The inhibition effects of 20(S/R)-notoginsenoside R2 on H22 hepatoma cells were assessed by CCK-8 and TUNEL assays, and the underlying mechanism was investigated by Western blotting. Lactiplantibacillus plantarum S165 could effectively transform notoginsenoside R1 to 20(S/R)-notoginsenoside R2 with a conversion yield of 82.85%. Our results showed that 20(S/R)-notoginsenoside R2 inhibited H22 hepatoma cells proliferation and promoted apoptosis. The apoptosis of H22 hepatoma cells was promoted by 20(S/R)-notoginsenoside R2 through the blockade of the PI3K/AKT/mTOR signaling pathway. The biotransformation method used in this study resulted in the production of 20(S)-notoginsenoside R2 and 20(R)-notoginsenoside R2 from notoginsenoside R1, and the anti-tumor activity of the transformed substance markedly improved.