Perfluoro compounds are widely used in various manufacturing processes, which leads to their bioaccumulation and subsequent adverse effects on human health. Using interface-selective vibrational spectroscopy (heterodyne-detected vibrational sum frequency generation (HD-VSFG)), we have elucidated the molecular mechanism of the perturbation of lipid monolayers on the water surface using a prototype perfluorinated persistent organic pollutant, perfluoroheptanoic acid (PFHA). PFHA disrupts the well-ordered all-trans conformation of a cationic lipid (1,2-dipalmitoyl-3-trimethylammonium propane (DPTAP)) monolayer and reduces the interfacial electric field at the lipid/water interface. In contrast, the hydrophobic packing of an anionic lipid (1,2-dipalmitoyl-sn-glycero-3-phospoglycerol (DPPG)) monolayer remains largely unaffected in the presence of PFHA, though the interfacial electric field is reduced. For a zwitterionic lipid (1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC))/water interface, both alkyl chain ordering and interfacial electric field are fairly perturbed by PFHA. Lipid headgroup-specific interaction of PFHA and the repulsive interaction of oleophobic fluoroalkyl chain with the lipid alkyl chains govern these distinct perturbations of the lipid monolayers on the water surface.