A novel open-tubular capillary electrochromatography (OT-CEC) with modified core/shell magnetic nanoparticles coating as stationary phase was introduced using external magnetic force to fix magnetic nanoparticles. The magnetic nanoparticles coating inside the capillary columns could be easily regenerated by removing and re-applying the external magnetic field. Magnetic field intensity, concentration and flow rate of nanoparticles suspension were investigated to achieve simple and stable preparation. Mixture of five organic acids was used as the marker sample to evaluate the OT-CEC system, and the relative column efficiency of anthranilic acid reaches 220,000 plates/m. The excellent within-column and between-column repeatability has been testified with the RSDs of retention time of less than 1.51 and 5.29%, respectively. The aqueous extract of rhizoma gastrodiae was analyzed by the OT-CEC system, and 23 peaks were eluted in 30 min. Compared with conventional open-tubular capillary column, this new system shows faster separation speed and higher column efficiency from the larger surface area of nanoparticles. It has great potential in the method development for the analysis of complex samples, since magnetic coating can effectively prolong the column life by expediently replacing stationary phase to eliminate the pollution or irreversible adsorption.