Colorless polyimide (CPI) films were modified by direct fluorination. The effects of fluorination duration on the chemical structure and surface physical morphology of CPI films were investigated in detail. The results show that direct fluorination induces significant changes in the surface composition and structure, leading to an enhancement in the F/C and O/C ratios. Fluoridation also resulted in increased surface microcracking. In comparison to the original CPI films, the fluorinated CPI films showed good thermal stability and higher glass transition temperatures (Tg), and higher optical transmittance (about 93.0%) in the ultraviolet–visible light region. Moreover, the fluorinated surfaces exhibit a high hydrophily and lipophilicity, and consequently a very high surface energy, according to contact angle measurements.