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 750 nm driven by −1.0 V (coloration) and +1 V (bleaching) with fast response times (coloration time: 13.58 s, bleaching time: 8.07 s) and a high coloration efficiency of 527 cm2 C−1. This study can supply useful and efficient avenue for designing flexible complementary electrochromic device for energy‐saving flexible electronics.