Regio- and 1,2-cis-stereoselective chemical glycosylation of unprotected glycosyl acceptors has been in great demand for the efficient synthesis of natural glycosides. However, simultaneously regulating these selectivities has been a long-standing problem in synthetic organic chemistry. In nature, glycosyl transferases catalyze regioselective 1,2-cis-glycosylations via the S(N)i mechanism, yet no useful chemical glycosylations based on this mechanism have been developed. In this paper, we report a highly regio- and 1,2-cis-stereoselective S(N)i-type glycosylation of 1,2-anhydro donors and unprotected sugar acceptors using p-nitrophenylboronic acid (10e) as a catalyst in the presence of water under mild conditions. Highly controlled regio- and 1,2-cis-stereoselectivities were achieved via the combination of boron mediated carbohydrate recognition and the S(N)i-type mechanism. Mechanistic studies using the KIEs and DFT calculations were consistent with a highly dissociative concerted S(N)i mechanism. This glycosylation method was applied successfully to the direct glycosylation of unprotected natural glycosides and the efficient synthesis of a complex oligosaccharide with minimal protecting groups.