Poly(3, 4-ethylenedioxythiophene):Polystyrene sulfonate (PEDOT:PSS) has good conductivity and can be easily dispersed in water. Coating the aqueous dispersion onto transparent films can be used to form ion storage layers for electrochromic devices (ECDs). However, the poor water resistance and flexibility of PEDOT:PSS conductive films limit their application in the field of flexible devices. In this paper the flexible hydrophobic molecule isopropylacrylamide (NIPAM) was applied to modify PEDOT:PSS. A series of poly ((styrene sulfonate)-co-isopropylacrylamide) P(SS-co-NIPAM) copolymers with different proportions of NIPAM was prepared, and the conductive polymer PEDOT:P(SS-co-NIPAM) was prepared by oxidative polymerization using P(SS-co-NIPAM) as template. Compared with the unmodified PEDOT:PSS film, when 15% NIPAM (molar fraction, based on the substance content of sodium styrene sulfonate) was added, the transmission rate of the film remained at 81.1%, the water contact angle increased from 18.5° to 39°, the hydrophobicity was improved, and after bending of 1000 times the change of square resistance of the film was 5.71 kΩ/sq , which was much smaller than that of the unmodified PEDOT:PSS film (10.60 kΩ/sq).The optical contrast (ΔT) of the electrochromic devices with PEDOT:P(SS-co-NIPAM) containing 15% NIPAM was 9.83%. After 800 cycles, the ΔT was 9.55%, which was decreased only 0.28%, the attenuation was comparable to that of the devices with unmodified PEDOT:PSS films as ion storage layer. The results indicated that NIPAM improved the flexibility and hydrophobicity of PEDOT:PSS conductive polymer, and the ECD devices using PEDOT:P(SS-co-NIPAM) as ion storage layer could maintain excellent electrochromic performance.