Regio- and stereocontrolled synthesis and conformational analysis of a series of benzimidazole nucleosides were achieved. A simple method by 1H NMR 1D NOE experiment was developed for estimation of syn or anti conformation of benzimidazole nucleosides. Substituents at C2 of benzimidazole demonstrated to play a key role both in the unexpected regioselectivity of the glycosidic reaction and in the conformation distributions of the final products.