A mixture of six biphenyl nitrile compounds and three related substances with high hydrophobicity and similar structures was successfully separated by microemulsion electrokinetic chromatography (MEEKC) within 30 min. The microemulsion system contained 100 mM sodium dodecyl sulfate (SDS), 80 mM sodium cholate (SC), 0.81% v/v heptane, 7.5% v/v n-butanol, 10% v/v acetonitrile, and 10 mM borate. The addition of SC, organic modifiers, sample preparation, and temperature all showed remarkable effects on the separation. The capacity factor (k) was calculated by using dodecyl benzene as the marker for microemulsion, and the calculated partition coefficient log P(o/w) of the solutes was in the range of 3.35-7.38. The log k values matched well with the log P(o/w) with a correlation coefficient of 0.96. In addition, the linear correlation coefficients of each compound between peak area and concentration were from 0.996 to 0.998 with the repeatability RSD value < 1.2% for migration time and < 4.8% for peak area, and the highest theoretic plate number was > 586000. MEEKC was compared with micellar electrokinetic chromatography (MEKC) indicating that the former method is more suitable for this separation and can be used for the quality control of biphenyl nitrile compounds in the synthesis of liquid crystals.