A copper ion imprinted chitosan flocculant (Cu2+@CTS) was synthesized by the molecular imprinting technique to improve the flocculation selectivity of chitosan to heavy metal ions. The effects of the amount of crosslinking agent, crosslinking time, temperature on the properties of the material were systematically investigated. Under the optimum preparation conditions, the flocculation rate and removal rate of Cu2+@CTS were 98.26% and 88.4%, respectively, 2.85 and 3.86 times higher than that of the unprinted chitosan flocculant. On this basis, the flocculation selectivity of Cu2+@CTS to Cu2+ in the presence of Zn2+, Ni2+ and other competitive ions was further explored. The experimental results indicated the removal rate of Cu2+ by Cu2+@CTS was as high as 70%–85%, which was 2.2–2.7 times that of other ions, while the removal rate of three metal ions by non‐imprinted chitosan flocculants was less than 35%. This study provided a reference for improving the selectivity of chitosan‐based flocculant to Cu2+.