Electrochromic smart windows play a significant role in energy saving technologies and there is a need to find more efficient as well as cheaper electrode materials suitable for this application. Electrode materials with adequate usage of nanostructuring and novel design strategies can help in improving the charge transfer and achieving better electrochromic performance. Herein, we explored a nanostructured electrode with the bilayer heterojunction design employing environmental friendly & cost effective TiO2 and MoO3 in an electrochromic device. A bilayer electrode with nanoparticulate TiO2 in the bottom layer and randomly oriented MoO3 nanostructures as the top layer has been adopted for the first time. The electrode exemplified a superior performance in terms of high current density and charge storage capacity as well as rate capability as compared to the relevant reports in the literature. A color contrast of 38%, switching response of ~2 s and high coloration efficiency of 72.5 cm2/C were achieved. The device has also shown good cyclic stability and high reversibility. The enhanced performance is ascribed to the nanostructured morphology of the electrode and the built-in potential at the interface, which improved the charge transfer, electrical conductivity and ionic transport in the device. The study presents a new viable approach of electrode design with nanoparticle bottom layer to improve the electrochromic performance capabilities, which can be extended to any other electrochromic materials as well.