The present invention provides a preparation method of deglycosylated ginsenosides, which uses the supercritical fluid technology to conduct the deglycosylation of ginsenosides extract in supercritical solvent under preset pressure and temperature conditions. Under the same operational conditions, the deglycosylated ginsenosides extract and solvent at supercritical state are input into an adsorption tank at the preset volume flow rate ratio for the adsorption of ginsenosides. Then, the adsorbed ginsenosides are applied with gradient eluent by using the ethanol solution. Finally, the pressure is lowered for the separation and purification of ginsenosides to get the deglycosylated ginsenosides of high concentration.