On-line preconcentration incorporating cation-selective exhaustive injection (CSEI) and sweeping followed by micellar electrokinetic chromatography (MEKC) was developed for the simultaneous determination of the bioactive alkaloids nuciferine and O-nornuciferine. The parameters affecting the analytical performance were systematically investigated. Under the optimal conditions, the enrichment factor was significantly improved by 7000 to 13000-fold compared with traditional MEKC. The analytes were well separated within 15 min. The limits of detection for nuciferine and O-nornuciferine were 4.00 and 2.00 ng∙mL−1, and the limits of quantification were 8.00 and 10.00 ng∙mL−1, respectively. The relative standard deviations for intra-day and inter-day precision were less than 3.0%. The recoveries of the analytes were from 98.9% to 102%. Furthermore, the developed method was demonstrated to be suitable for the analysis of nuciferine and O-nornuciferine in lotus leaves, offering high performance without the loss of resolution. CSEI-sweeping-MEKC provides a simple, environmental-friendly option for preconcentration and quantification of nuciferine and O-nornuciferine.