Verapamil is a commonly used medicine for the treatment of supraventricular arrhythmias, angina and hypertension. Recently, some newly developed applications of Verapamil, such as treating hypomania and chemotherapy for cancers, have been reported. Thus, monitoring the concentration of Verapamil accurately is very important. The major clinical analytical methods of Verapamil concentration determination are high performance liquid chromatography (HPLC) with UV or with fluorescence detector. However, these analytical methods have some disadvantages, like expensive instruments, complex operation, and time-consuming etc. The chemical structure and properties of Verapamil are very stable. The preliminary result of electrochemical analysis doesn¡¦t show any electrochemical activity. In this study, we developed an innovative ozone pre-treatment method to oxidize Verapamil to the smaller molecules and change its structure. Verapamil have excellent electrochemical activity after ozone pre-treatment. The spectroscopy and mass spectrometry show the changes of Verapamil structure. The products of Verapamil treated with ozone are also predicted by mass spectrometry. The gold nanoelectrode ensemble electrodes (GNEE) are used as working electrode for its good catalytic activity of electrochemical reaction, high sensitivity and high selectivity. The overall experimental framework of this study is microchip with GNEE working electrode accompanied by cyclic voltammetry, an electrochemical analytical instrument. Compared with traditional analytical methods, the system has some advantages such as small size, micro sample volume, easy operation, rapid detection and low cost. The limit concentration of Verapamil solution for stable detection in the system is 10 ng/mL. A linear dynamic range with a high correlation factor from 10 ng/mL to 100 £gg/mL was obtained. For the analysis of serum sample, Verapamil present excellent electrochemical activity at 1 ng/mL. A linear dynamic range with a high correlation factor from 1 ng/mL to 100 £gg/mLwas obtained. According to the results, our system for clinical Verapmil concentration analysis has the feasibility of the practical application.