β-N-Acetylhexosaminidases (HEXs) play important roles in human diseases and the biosynthesis of human milk oligosaccharides. Despite extensive research, the catalytic mechanism of these enzymes remains largely unexplored. In this study, we employed quantum mechanics/molecular mechanics metadynamics to investigate the molecular mechanism of Streptomyces coelicolor HEX (ScHEX), which has shed light on the transition state structures and conformational pathways of this enzyme. Our simulations revealed that Asp242, located near the assisting residue, can switch the reaction intermediate to an oxazolinium ion or a neutral oxazoline, depending on the protonation state of the residue. Moreover, our findings indicated that the free energy barrier of the second-step reaction starting from the neutral oxazoline increases steeply due to the reduction in the anomeric carbon positive charge and the shortening of the C1-O2N bond. Our results provide valuable insights into the mechanism of substrate-assisted catalysis and could facilitate the design of inhibitors and the engineering of analogous glycosidases for biosynthesis.