Abstract: This paper introduced the present situation of biological catalysis in non-aqueous phase. The common biological catalysts including free enzyme, immobilized enzyme and whole cell catalyst were presented in detail. Four kinds of catalytic media in non-aqueous phase including organic solvent system, solvent-free system, ionic liquid system and supercritical fluid medium system were described. And the deglycosylation, glycosylation, acylation modifications and methylation of glycoside compounds were expounded. This paper also described the effects of structural modification on the properties of the compounds, such as improving the solubility, enhancing the stability and promoting the biological activity of these compounds. The related applications of glycoside compounds with structural modification were briefly introduced.