Efficient and selective binding of perfluorocarbons (PFCs), comprising only fluorine and carbon atoms, unlike hydrocarbons, remains quite difficult owing to the repulsive nature of fluorine. Here we describe that a cavity modulation strategy enables metal-linked polyaromatic capsules to quantitatively bind PFCs with excellent selectivity. From a mixture of perfluoroarene and the corresponding perfluoroalkane (i.e., perfluoronaphthalene and perfluorodecalin), a Pt(II)-linked capsule exclusively binds the arenes in water at room temperature, via effective D-A-A-D π-stacking interactions. The size-selective binding toward perfluoroarenes (i.e., perfluoronaphthalene and perfluorobenzene) is improved by using the analogous N-doped capsule from 85% to quantitative selectivity. Furthermore, unlike the Pt(II)-capsule, an isostructural Pd(II)-linked capsule displays the unusual length/shape-selective binding of linear/cyclic perfluoroalkanes (i.e., perfluoroheptane and perfluorodecalin) under similar conditions. Recognition of substituted hydrogen atoms on perfluorobiphenyl can also be accomplished using the Pt(II)-capsule. Various PFCs are thus clearly distinguished for the first time by the modulable polyaromatic capsules under ambient aqueous conditions.