[Objective] Hydrolysis of ginkgo flavonoid glycosides by microbial β-glucosidase is less known. Therefore, we screened a microbial β-glucosidase with high enzymatic activity to hydrolyze ginkgo flavonoids and analyze its substrate-specificity. [Methods] β-Glucosidases with high enzymatic activity for the hydrolysis of ginkgo flavone glycoside were screened from traditional fermented soybean meal in Guizhou using Ginkgo biloba extract as the sole carbon source. The strain producing glucosidase was then identified, and the selectivity of the enzyme to different substrates was compared. The Michaelis constant Km and maximum velocity Vmax of the enzymatic reaction to hydrolyze ginkgo flavonoids were determined. Finally, the substrate-specific mechanism of the enzyme was analyzed via molecular docking studies. [Results] Among the strains observed, strain GUXN01 showed the highest β-glucosidase activity and was subsequently identified as Bacillus subtilis. β-glucosidase produced by GUXN01 had broad substrate specificity to sugars and glycosides with the β configuration. The glucosidase showed especially good affinity to ginkgo flavonoid glycosides. Molecular docking studies indicated that B. subtilis β-glucosidase had different affinities and selectivities toward ginkgo flavonoid glycosides and other glycosides due to differences in the interactions between the enzyme and substrate structures. [Conclusion] These findings may serve as a good foundation for the production of the corresponding aglycones via the hydrolysis of ginkgo flavonoid glycosides through the β-glucosidase produced by GUXN01.