In this study, three different oil phases include 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide (BMPy[NTf]), 1-butyl-3-methylimidazolium hexafluorophosphate (BMImPF) and n-octane were compared for the MEEKC analysis (SDS as surfactant and n-butanol as co-surfactant) of eight isoflavones from pueraria. The investigated isoflavones can be well separated by all of those three microemulsion systems after careful optimization, and the MEEKC with n-octane as the oil phase was the best choice (good symmetry and high resolutions of peaks with short analysis time) for the analysis. The optimum conditions of MEEKC method were as follows: 70 mM SDS, 0.7 M n-butanol and 0.5% (w/v) n-octane in 10 mM sodium tetraborate (STB) at pH 8.5, applied voltage was 23 kV and cassette temperature was set at 30°C. And then the developed method was fully validated (limit of detection, limit of quantification, intraday precision, interday precision and recovery) and successfully applied to determine the eight analytes in three Radix Puerariae samples. In addition, although the MEEKC with classic oil phase (n-octane) showed better results for isoflavones analysis in this study, the MEEKC with ionic liquids (BMPy[NTf] and BMImPF) also showed great separation potential for analytes, which may be further applied in the analysis of other natural products.