This research compares as-synthesized W18O49 sub-stoichiometric bundled nanowires and commercial WO3 nanoparticles, aiming to understand their general electrochromic behavior differences. The effect of low temperature annealing on the electrochromic performance of the tungsten oxide (WOx) thin film samples at 250 to 350 °C was investigated. We elucidate the fundamental aspects of the heat treatment-structure-performance relationship. We have found that the annealing treatment at low temperatures can improve the optical modulation and durability of the WOx thin films, without changing the structure and morphology of the as-synthesized samples. We also discuss the effect on the degradation behavior of electrochromic devices with regards to the Li+ trapping/de-trapping.