Herein, one water-soluble functionalized ionic liquid (IL), 1-butyl-3-methylimidazolium dodecanesulfonate (BAS), was designed, investigated and successfully applied to microchip micellar electrokinetic chromatography (MEKC) construction. It possessed the properties of both IL and surfactant. A fairly stable pH value approximately 7.4, which was fit to pH values of general biological buffers, was nicely placed at the optimum concentration of 20mM BAS solution. While applying BAS solution as running buffer in poly(dimethylsiloxane) (PDMS) microfluidic systems, significantly enhanced electroosmotic flow (8-fold) and resolutions between analytes were obtained than that using other supporting electrolytes or surfactants. Pure BAS solution could conveniently complete the task of MEKC establishment: not only the ionic strength of the running buffer was guaranteed, but also the analytes adsorption to PDMS surface was conquered, as was demonstrated in the sensitive determination of fluorescent dyes and well-separated protein mixtures.