[Background] Microbial transformation is an important means for structural modification of natural products. Many microorganisms can transform ginsenoside compounds into saponins with high activity by modifying the structure of different positions.[Objective] To screen a strain that can transform ginsenoside Rb1 into rare ginsenosides with high pharmacological activity. [Methods] A total of 36 fungal strains were isolated from rhizosphere soil and stem of Panax notoginseng and purified. Primary screening of saponin transformation activity was performed with β-glucosidase method, followed by a second screening with ginsenoside Rb1 as substrate. The transformation products were analyzed by TLC, HPLC, and MS. [Results] A strain F17 with high transformation activity of ginsenoside Rb1 was screened out and it was identified as Pestalotiopsis biciliata based on morphological observation and ITS sequence analysis. It can transform ginsenoside Rb1 into ginsenoside Rd and rare ginsenosides F2 and C-K through the pathway of Rb1→Rd→F2→C-K. [Conclusion] This study provides a new strain for transformation of rare ginsenosides F2 and C-K.