Microemulsion electrokinetic chromatography (MEEKC) has been used to indirectly measure octanol-water partition coefficients (log P(ow)) of compounds. In order to obtain an accurate log P(ow) value, the electrophoretic mobilities of the microemulsion phase (mu(me)) and the analyte (mu(eff)) in MEEKC must be accurately required. However, in conventional MEEKC, the shortage of obtaining mu(me) with a tracing method was discovered, and the influences of concentration, injection volume of analyte, and high electric field on measuring mu(eff) were also found. In this paper, a novel method called improved MEEKC (I-MEEKC) was developed to avoid the problems mentioned above. In I-MEEKC, a nonlinearity fitting program was used to obtain mu(me) to avoid the error from tracing mu(me); the extrapolating method was used to eliminate the effects of concentrations and injection volumes of analytes on mu(eff) measurement, and an enough stable microemulsion was selected to eliminate the effect of high electric field on mu(eff )measurement. Then the novel method was applied to estimate log P(ow) of uncharged compounds and charged pharmaceuticals compared to the conventional MEEKC. The log P(ow) of all analytes obtained by I-MEEKC agreed with those obtained by classical shake flask or literature values, the errors between them were within 0.1 logarithm units, better than the ones by conventional MEEKC.