To clarify proton conduction mechanism in protic ionic liquids (PILs) and pseudo-PILs (pPILs), equimolar mixtures of N-methylimidazole (C(1)Im) with fluorinated acetic acids were investigated by Raman spectroscopy, X-ray scattering, and dielectric relaxation spectroscopy (DRS). Only the ionic species exist in the equimolar mixture of C(1)Im and HTFA (HTFA: trifluoroacetic acid). On the other hand, the equimolar mixture of C(1)Im and HDFA (HDFA: difluoroacetic acid) consists of both ionic and electrically neutral species. In particular, not only the electrostatic but also van der Waals interactions with the F atoms were observed in the liquid structures of both [C(1)hIm(+)][TFA(-)] and [C(1)hIm(+)][DFA(-)]. The concept for proton conduction mechanism that we have proposed in previous study was revisited; the proton conduction mechanism could be classified with two linear free energy relationship lines for proton exchange reaction and translation/rotation of proton carriers. Our results exhibit that the proton conduction mechanism changes from proton hopping to vehicle mechanism with increasing acidity of an acid HA in PILs.