Single crystalline ZnO nano-array films are prepared by electrochemical deposition process, which are successfully introduced as an interlayer between FTO conductive glass substrate and TiO2 nanoparticle films to fabricate the quantum dot sensitized solar cells. Different structure of ZnO nano-array films are modulated by the time of electrochemical deposition process, which have been mainly investigated the photovoltaic performance and charge transfer property of the solar cells. The enhancements of optical absorption properties and electron-hole separation properties on photo-electrodes have been observed by UV–Vis absorption and photoluminescence spectra. And electrochemical impedance spectra and photoluminescence decay analysis have indicated that the ZnO nano-array interlayer can effectively increase the rate of charge transfer in the quantum dot sensitized solar cells system. With the balance on the diameter, density and thickness of the ZnO nano-array interlayer, the photovoltaic conversion efficiency of FTO/ZnO/TiO2/CuInS2 quantum dot sensitized solar cells have enhanced from 4.12% to 4.58% without any optimization of passivation, electrolyte and counter electrode.