Amphiphobic fluoroalkyl chains are exploited for creating robust and diverse self‐assembled biomimetic catalysts. Long terminal perfluoroalkyl chains (CnF2n+1 with n=6, 8, and 10) linked with a short perhydroalkyl chains (CmH2m with m=2 and 3) were used to synthesize several 1,4,7‐triazacyclononane (TACN) derivatives, CnF2n+1‐CmH2m‐TACN. In the presence of an equimolar amount of Zn2+ ions that coordinate the TACN moiety and drive the self‐assembly into micelle‐like aggregates, the critical aggregation concentration of polyfluorinated CnF2n+1‐CmH2m‐TACN⋅Zn2+ was lowered by ∼1 order of magnitude compared to the traditional perhyroalkyl counterpart with identical carbon number of alkyl chain. When 2’‐hydroxypropyl‐4‐nitrophenyl phosphate was used as the model phosphate substrate, polyfluorinated CnF2n+1‐CmH2m‐TACN⋅Zn2+ assemblies showed higher affinity and catalytic activity, compared to its perhyroalkyl chain‐based counterpart. Coarse‐grained molecular dynamic simulations have been introduced to explore the supramolecular assembly of polyfluoroalkyl chains in the presence of Zn2+ ions and to better understand their enhanced catalytic activity.