Most glycosides in herbal medicines become pharmacologically active after hydrolysis or subsequent metabolism to respective aglycones. Hence, the hydrolytic efficiency of glycosidase is a crucial determinant of the pharmacological efficacy of herbal glycosides. In this study, we investigated the enzymatic conversion of the four herbal extracts and their glycosides using the glycoside hydrolase family 3 β-glucosidase from Lactobacillus antri (rBGLa). We show that β-glucosidase substrate specificity depends on the arrangements and linkage types of sugar residues in glycosides. The enzyme rBGLa showed higher hydrolytic selectivity for glucopyranoside than for glucuronide and rhamnopyranoside, and specificity for 1→6 rather than 1→2 linkages. In addition, in silico 3D structural models suggested that D243 and E426 of rBGLa act as catalytic nucleophile and acid/base residues, respectively. These experiments also suggested that substrate specificity is determined by interactions between the C6 residue of the sugar moiety of the substrate glycoside and the oxygen OD1 of D56 in rBGLa. Therefore, despite the broad substrate spectrum of β-glucosidase, differences in hydrolytic selectivity of β-glucosidases for glycoside structures could be exploited to enhance the hydrolysis of the desired medicinal glycosides in herbs using tailored β-glucosidases, allowing for improvement of specific potencies of herbal medicines.