Herein, one water-soluble functionalized ionic liquid, 1-butyl-3-methylimidazolium dodecyl sulfate ([BMIm(+)][C12H25SO4-]), was designed and its superiorities either used as supporting electrolytes or as additives for successful establishment of MEKC with electrochemiluminescence (ECL) detection (MEKC-ECL) method were investigated. Compared with the common supporting electrolytes such as phosphate solution, 1-butyl-3-methylimidazolium dodecyl sulfate solution used as running buffers led to greatly enhanced ECL intensities and column efficiencies for negative targets, a little increase for neutral-charge ones while maintained nearly unchanged for positive ones due to the electrostatic forces between the large cation BMIm(+) and the solutes and the hydrophobic interactions resulting from the large anion C12H25SO4. Moreover, resolution efficiency between analytes was significantly improved. As the existence of ionic liquid moiety, BMIm(+), accelerated the electron transfer at the electrode surface, the poisoning effect of long chain C12H25SO4 on the electrode surface was eliminated and reproducible ECL intensifies with relative standard derivation of 1.02% (n = 6) were obtained. The proposed novel MEKC-ECL system was again validated by the baseline separated two similar amino acids of proline and hydroxyproline with lower detection limits of 0.5 and 0.8 mu M (S/N = 3), respectively.