A novel method for the rapid separation and determination of five polar 5-nitroimidazoles in water from different sources by pressurized capillary electrochromatography has been developed. Compared with the gradient elution mode and the packed nonpolar columns which were usually utilized for the separation of 5-nitroimidazoles, a simple isocratic elution mode and low-cost homemade polar molecularly imprinted polymer monolith were used in the experiment. Electrochromatographic conditions such as pH of buffer, organic modifier, concentration of buffer, and separation voltage were optimized. At 320 nm UV wavelengths, the five 5-nitroimidazoles could be baseline-separated rapidly in less than 11 min with the separation voltage of +20 kV in 10 mmol/L sodium dihydrogen phosphate-disodium hydrogen phosphate buffer solution (pH 4.82) containing 30% acetonitrile. Under the optimum conditions, the linear ranges of the metronidazole, secnidazole, tinidazole, ornidazole, and metronidazole benzoate were 0.50–100.00, 0.50–100.00, 0.80–500.00, 0.80–100.00, and 5.00–500.00 μg/mL, respectively, and the detection limits of these analytes were 0.11–0.73 μg/mL. Column efficiencies of 43 000, 36 000, 34 000, 14 000, and 29 000 plates/m were obtained for metronidazole, secnidazole, tinidazole, ornidazole, and metronidazole benzoate, respectively. The recoveries of different water samples were about 85.0–95.8%. Additionally, the proposed method has been successfully applied to the rapid separation of 5-nitroimidazoles in the locally available pure milk sample by simple pretreatment.