The root of ginseng is a famous functional food and a herbal medicine. Research into the development of a method for increasing the pharmaceutical effect of ginseng by conversion of ginsenosides, the major active components of ginseng, by high-temperature and high-pressure thermal processing has been conducted. However, changes in the structures of each ginsenoside by heat processing and their contributions to anticancer activity have not yet been fully elucidated. Here, we investigated whether anticancer activity of ginsenosides, such as Rb1, Rb2, Rc, Rd, and Re, was associated with changes in the structures of each ginsenoside by heat processing in human stomach cancer AGS cells. Upon heat processing at 120 °C, most peaks of ginsenosides Rb1, Rb2, Rc, and Rd disappeared and the contents of less-polar ginsenosides 20(S,R)-Rg3, Rk1, and Rg5 were newly detected. From the quantitative analysis of ginsenosides, the generated amounts of less-polar ginsenosides were the highest after heat processing of ginsenoside Rd. After heat processing, the diol-type ginsenosides Rb1, Rb2, Rc, and Rd gained significant antiproliferative activity. In particular, ginsenoside Rd induced the strongest cell death among the diol-type ginsenosides, whereas the triol-type gisenoside Re showed weak antiproliferative activity. Ginsenoside Rd-induced cell death was associated with caspase-dependent apoptosis. Taken together, these results demonstrate that deglycosylation of Rd contributes to improved anticancer activity of ginseng and provide new insight on the mechanism of increased anticancer effects of ginsenosides upon heat processing.