In this paper the structural and vibrational properties of intercalated fluorine graphite (C4F)n under compression up to 40 GPa are investigated by means of Raman spectroscopy, X-ray diffraction and ab initio calculations. The theoretical study was performed within the framework of the density functional theory, taking into account van der Waals corrections to the total energy. We studied the effect of anisotropic and isotropic deformation on the crystal properties, in relation to the layered structure of the sample and in particular to the CF bonding. The evolution with pressure of the phonon modes at the center of the Brillouin zone was calculated and compared with experimental data. Both our experimental data and theoretical models indicate that a structural transition occurs around 10 GPa. Above this pressure the (C4F)n structure becomes dynamically unstable, characterized by a “soft mode” and a change in symmetry due to anisotropic strain components.