The influence of counterions on micellization of perfluorononanoic carboxylate ammonium salts in water and 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]BF4) solutions was investigated by surface tension and F-19 NMR measurements and freeze-fracture transmission electron microscopy (FF-TEM) observations. Changes in the counterions of the fluorocarbon surfactants have different effects on the two solvents. With the increase of counterion volume, the critical micelle concentration (cmc) value of relevant fluorinated surfactant decreases in aqueous solutions. This is because the counterions with larger size, such as N+(CH3)(4), can be little hydrated, which can screen the electrostatic repulsion of the headgroups of the fluorocarbon surfactant and thus facilitate micelle formation. However, the fluorocarbon surfactants can dissolve and form micelles in [bmim]BF4 only when they provide with largest counterion such as N+(CH3)(4). This is because the counterion, N+(CH3)(4), disperses the charge of the cations, which could weaken the electrostatic interaction between the ion pair of the surfactant, leading to a higher degree of counterion binding. The thermodynamic parameters estimated from the temperature dependence of the cmc values tell us that the micelle formation for tetramethylammonium perfluorononanoic carboxylate (C8F17COON(CH3)(4), PFNT) in ionic liquids (ILs) is an entropy-driven process at low temperature but an enthalpy-driven process at high temperature. The driving force of the micellization for fluorocarbon surfactants in [bmim]BF4 is the solvophobic effect, due to the hydrophobic and oleophobic properties of fluorocarbon chains.