Tungsten trioxide-poly(3,4-ethylenedioxythiophene) (WO3-PEDOT) and tungsten trioxide-polyfuran (WO3-PFu) were prepared by rf rotating plasma polymerization. Electrochromic hybrid thin films were fabricated onto flexible polyethylene terephthalate (PET)/ indium tin oxide (ITO) film using electron beam evaporation method. In order to deeply characterize all films, scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS) and electrochemical impedance spectroscopy (EIS) techniques were used. The counter electrode effect on plasma modified WO3 nano hybrids-based electrochromic devices (ECDs) was evaluated. By incorporating flexible vanadium pentoxide (V2O5) film as counter electrode, complementary ECDs were constructed through combining the hybrid flexible films (WO3-PEDOT, WO3-PFu) as working electrodes, which exhibit highly efficient electrochromic performance with low voltage operation. Especially, WO3-PEDOT/V2O5-based ECD owns a high optical modulation of 61.5% at 750nm driven by -1.0V (coloration) and +1V (bleaching) with fast response times (coloration time: 13.58s, bleaching time: 8.07s) and a high coloration efficiency of 527cm(2)C(-1). This study can supply useful and efficient avenue for designing flexible complementary electrochromic device for energy-saving flexible electronics.