Metals are essential components of all living cells, and in many cases cells trigger and utilize dynamic metal movements for signaling purposes. So, it is very critical to develop the biosensors for determination of metal ions in living systems with high selectivity and accuracy. In this work, taking Cu(2+) as a model, an accurate and selective ratiometric electrochemical biosensor was developed. First, the specific molecule, 2,2',2″-(2,2',2″-nitrilotris(ethane-2,1-diyl)-tris((pyridin-2-ylmethyl)azanediyl)triethanethiol (TPAASH), was designed and synthesized for specific recognition of Cu(2+). Meanwhile, electroactive molecule, 6-(ferrocenyl)hexanethiol (FcHT) was coimmobilized with TPAASH at one electrode as inner reference molecule to provide a built-in correction for avoiding the environmental effects. Thus, the developed biosensor demonstrated high accuracy and remarkable selectivity toward Cu(2+) against other metal ions, amino acids, and so on. In addition, the biosensor also showed high sensitivity due to the electrocatalytic activity of the nanostructured gold flowers. As a result, the present ratiometric electrochemical biosensor was successfully applied in detection of Cu(2+) in brain microdialysates of normal rat brain and that followed by global cerebral ischemia.