Rare dehydrated ginsenosides barely exist in natural ginseng plants. Herein, the confined microwave technique was utilized to transform the main ginsenosides of Panax notoginseng leaves (PNL) into dehydrated ginsenosides. The main microwave-treated products of dried PNL are dehydrated ginsenoside Rk1, Rg5, notoginsenoside SFt3, and SFt4. Comparatively, the main microwave-treated products of water preimmersed PNL are dehydrated ginsenoside Rk2, Rh3, notoginsenoside SFt3, and SFt4. The impacts of solvent, solid-liquid ratio, microwave temperature and duration on the yield of dehydrated ginsenosides were explored. Based on theoretical calculation, primary ginsenosides in water preimmersed PNL are more prone to deglycosylation at the C-20 site and dehydration elimination reactions at the side chain during microwave treatment. Moreover, reference compounds were used to verify ginsenoside transformation pathway, and the dehydrated ginsenosides were individually purified and identified. In short, this study elucidates novel approach for preparing rare Δ20(21)- and Δ20(22)-dehydrated protopanoxadiol ginsenosides.