We used natural resources of halloysite nanotubes and alginate to prepare a novel porous adsorption material of organic–inorganic hybrid beads. The adsorption behaviour of Cu(II) onto the hybrid beads was examined by a continuous fixed bed column adsorption experiment. Meanwhile, the factors affecting the adsorption capacity such as bed height, influent concentration and flow rate were investigated. The adsorption capacity (Q0) reached 74.13 mg/g when the initial inlet concentration was 100 mg/L with a bed height of 12 cm and flow rate of 3 ml/min. The Thomas model and bed-depth service time fitted well with the experimental data. In the regeneration experiment, the hybrid beads retained high adsorption capacity after three adsorption–desorption cycles. Over the whole study, the new hybrid beads showed excellent adsorption and regeneration properties as well as favourable stability.