We present effects of counter anions on electrochromic behavior of asymmetrically substituted viologens, 1-hexyl-1'-nonafluorohexyl viologens (HERFVs). For this purpose, two anions, hexafluorophosphate ([PF6](-)) and bis(trifluorosulfonyl)imide ([TESI](-)), were employed for both HERFVs and 1-butyl-3-methylimidazolium ([BMIM](+))-based ionic liquids. The HERFV-containing electrochromic devices (ECDs) exhibited apparent dependence on the counter ions in terms of optical contrast, switching speed, long-term cyclic stability, coloration efficiency, and memory effect. Specifically, the ECDs based on [HERFV][PF6](2) showed a redox response at -1.0 V with a color change from colorless to blue. Meanwhile, the coloration of [HERFV] [TFSI](2) appeared at - 3.0 V, and a significantly long optical memory effect was observed with unstable cyclic repeatability. We attributed this discrepancy to the nature of counter ions, such as size and electronegativity, which may influence the electron transfer process during redox reactions. These results demonstrated that counter anions can exert a significant impact on the EC behaviors of asymmetrically substituted viologens. The presented approach suggests a potential tool for controlling EC properties of viologen derivatives for applications in transmissive windows and eye wear.