Due to the significant role of copper(II) ions in many biochemical and physiological processes, sensitive detection of copper(II) ions has attracted great attention. A novel quantitative copper(II) ion sensor is developed based on the conformational change of Cu2+ binding peptides using surface plasmon resonance (SPR) spectroscopy. The specific interaction between carboxyl groups of the peptide and Cu2+ induces a conformational change from α-helix to β-sheet with decreasing hydrophilicity. The formation of Cu2+–peptide aggregates on the chip surface leads to a refractive index change, which results in a sensitive SPR signal change. Thus, Cu2+ can be measured selectively and sensitively due to the conformational change of Cu2+ specific binding peptides. With this well-designed sensing platform, the detection range of copper(II) ions is found to be 1 × 10−12 M to 1 × 10−6 M with a detection limit of 0.44 pM, which is 3 orders of magnitude lower than that in previous reports. The copper(II) ion sensor designed in this study is proposed for application in biological and environmental analysis.