Two strains of fungi producing β-glucosidase were screened and identified from Martianus dermestoides. The conversion of rare ginsenosides and fermentation quality were improved by combined fermentation of the two strains. The dynamic fermentation process was studied, and the mechanism of ginsenoside transformation was clarified. Screening was performed by MRS (aesculin, ferric citrate) medium. Two fungi producing β-glucosidase were identified by 18S rRNA gene amplification. The strains were fermented with total ginsenoside, the fermentation products were analyzed by LC-MS/MS. Two fungi producing β-glucosidase were identified as genus Chaetomium and Aspergillus respectively. The fermentation products of WY1 reacted with total ginsenosides were Rd and Rh1. The fermentation products of WY2 reacted with total ginsenosides were Rd, Rh1, Rg3 and compound K. The conversion rates of Rh1, Rg3 and compound K were improved by WY1/ WY2 combined fermentation. The transformation path was Re→Rg1→Rh1; Rf→Rh1; Rb1/Rb2/Rc→Rd→Rg3/compound K. Protopanaxadiol-type ginsenosides were more easily converted than protopanaxatriol-type ginsenosides and most of the products are Rg3.