β‐CD‐NH2‐Fe3O4 magnetic nanomaterials were prepared and the electrochemical sensor was constructed using β‐CD‐NH2‐Fe3O4 magnetic nanomaterials modified GCE to determine toxic heavy metals(Pb2+, Cu2+) in river water. SEM, XRD and FTIR were used to characterize the structure and phase of β‐CD‐NH2‐Fe3O4. DPV results indicated that β‐CD‐NH2‐Fe3O4 modified GCE possessed large active area and excellent electron transfer. Under the optimum conditions, the peak current was proportional to the ion concentration in the range of 40 nM∼10 μM. LOD of Pb2+ and Cu2+ in this method was 1.71 nM and 1.57 nM, respectively. Compared with other similar results reported in the literature, the β‐CD‐NH2‐Fe3O4 modified electrode exhibited wider linear response range while with comparable lower LOD. It also exhibited excellent stability, reproducibility and anti‐interference ability.