The binding mechanism of iminosugar inhibitor 1-deoxynojirimycin and isofagomine toward β-glucosidase was studied with nanosecond time scale molecular dynamics. Four different systems were analyzed according to the different protonated states of inhibitor and enzyme (acid/base carboxyl group, Glu166). The simulations gained quite a reasonable result according to the thermodynamic experimental fact. Further conclusions were made including the following: (1) 1-deoxynojirimycin binds with the β-glucosidase as conjugate acid forms; (2) the slow onset inhibition of isofagomine aims to slow deprotonation of the acid/base carboxyl group which is caused by a nearly zero hydrogen bond interaction between the hydroxyls of the acid/base carboxyl group; and (3) the nucleophile carboxyl group plays an important role when the inhibitor binds with glucosidase.