Cell ion channels, cell proliferation and metastasis, and many other life activities are inseparable from the regulation of trace or even single copper ion (Cu
+
and/or Cu
2+
). In this work, an electrochemical sensor for sensitive quantitative detection of 0.4−4 amol L
−1
copper ions is developed by adopting: (1) copper ions catalyzing the click-chemistry reaction to capture numerous signal units; (2) special adsorption assembly method of signal units to ensure signal generation efficiency; and (3) fast scan voltammetry at 400 V s
−1
to enhance signal intensity. And then, the single-atom detection of copper ions is realized by constructing a multi-layer deep convolutional neural network model FSVNet to extract hidden features and signal information of fast scan voltammograms for 0.2 amol L
−1
of copper ions. Here, we show a multiple signal amplification strategy based on functionalized nanomaterials and fast scan voltammetry, together with a deep learning method, which realizes the sensitive detection and even single-atom detection of copper ions.