A novel capillary with hydroxyapatite (HAP) as the stationary phase was prepared for open-tubular capillary electrochromatography (OT-CEC). To immobilize HAP, a mussel-inspired polydopamine method was utilized to modify the capillary firstly, generating a polydopamine layer; and then a layer of HAP would be formed on the polydopamine layer by a biomineralization process, to produce a HAP-modified capillary (HAP@capillary). Scanning electron microscopy (SEM), energy dispersive X-ray spectrometry (EDS) and X-ray photoelectron spectroscopy (XPS) provided evidence of nanostructured HAP grown on the surface of the capillary wall. The electroosmotic flow (EOF) characteristic of the HAP@capillary was investigated by varying the percentage of acetonitrile and pH value of the buffer with thiourea as a marker, and a pH-dependent EOF from anode to cathode was observed. The HAP@capillary exhibits high column efficiency for methylbenzene, up to 151 138 plates per meter. Different kinds of compounds including alkylbenzenes, phenols and amines have been successfully separated by the HAP@capillary in CEC mode. The HAP@capillary also possessed good separation ability in capillary liquid chromatography (CLC) mode because of the relatively large ratio of HAP in the capillary; however, the separation efficiency was not as good as that in CEC mode. The reproducibilities of the HAP@capillary were evaluated, and the relative standard deviations were found to be lower than 5%.