In traditional practices, roots of ginseng and notoginseng are directly eaten as tonics or for the prevention and treatment of chronic diseases in the elderly. Research indicates that the bioactive secondary metabolites of ginseng and notoginseng are mainly ginsenosides. Ginsenosides exhibit a broad spectrum of preventive and therapeutic effects on various diseases related to the immune, nervous, and cardiovascular systems. Effective absorption and utilization of ginsenosides has been reported to require deglycosylation in the intestinal tract, where the intestinal microbiota plays a pivotal role. Some probiotics and gut microorganisms, including Lactobacillus and Bifidobacterium, can convert ginsenosides and produce β-glucosidases of glycoside hydrolases (GH) 1 and GH3, β-xylosidases of GH30 and α-L-arabinosidases of GH3 and GH51, which catalyze the hydrolysis of sugar moieties in ginsenosides. This review summarizes the research progress on the conversion of ginsenosides by probiotics and gut microorganisms and their enzymes. Furthermore, molecular docking analysis was used to elucidate the tertiary structures and active sites of GH1, GH3, GH30, and GH51 enzymes responsible for substrate interactions, offering valuable insights into the pivotal role of probiotics and gut microorganisms in the conversion of ginsenosides.