The aqueous solution of a kind of room-temperature ionic liquids (RTILs), 1-ethyl-3-methylimidazolium-tetrafluoroborate (1E-3MI-TFB), demonstrated its exclusive electro-osmotic property in microchip electrophoresis. It was applied as the working electrolyte for chiral separation in glass microchip electrophoresis. Compared with boric acid buffer, 1E3MI-TFB aqueous solution exhibited a broader separation window for enantiomers of dipeptides. Then the influences of chiral selector, pH and concentration on efficiency of chiral separation were discussed in detail. The unique mechanism of the generation of EOF was explored in a glass microcbannel using 1E-3MI-TFB aqueous solution as working electrolyte. A possible status of 1E-3MI cation in water was suggested at the first time, which facilitated the explanation of EOF and its characteristics in glass microchannel. Additionally, microchip electrophoresis using 1E-3MI-TFB aqueous solution was successfully applied to the chiral separation of complex enantiomers of dipeptides. RTILs aqueous solution, as the electrolyte for the separation of complicated optical isomers, could lead to a revolution in the analytical methods of chiral or conformational analysis for biomolecules.