To understand the role of structure imperfections on the performance of electrochromic transition metal oxide (ETMO) is challenging for the design of efficient smart windows. Herein, we investigate the performance evolution with tunable crystallographic imperfections for rutile TiO2 nanowire film (TNF). Structure imperfections, originating mainly from the copious oxygen deficiency, are apt to cumulatively retard the shuttling ions, resulting in the response rate for raw TNF being less than the half that of TNF annealed at 500 °C. We describe ion accommodation sites as a convolution of normal site and abnormal site, in which the normal site performs reversible coloration but the abnormal site contributes only to charge storage, which gives a rationale for the non-linear coloration and rate capability loss. These findings give a clear picture of the ion shuttling process, which is insightful for enhancing the electrochromic performance via structure reprogramming.