Higher biocidability of fluorinated quaternary ammonium salt (QAS) is usually contributed to its preferential segregation to the surface to better contact with and kill bacteria. However, whether its structure also elicits better performance is still unclear. Herein, the same amount of a fluorinated QAS and its nonfluorinated counterpart are both immobilized on the top surface to eliminate the effect of concentration distribution to only study their structure-biocidability relationship. Briefly, the fluorinated and nonfluorinated QASs were synthesized by quaternization of N,N-dimethylethanolamine with 2-(perfluorooctyl)ethyl bromide that was prepared by bromination of 2-(perfluorooctyl)ethanol and 1-bromodecane, respectively. Polystyrene (PS) and diblock copolymer poly(styrene)-b-poly(tert-butyl acrylate) (PS-PtBA) were successively spin coated on SiO2 wafers at different concentrations to form bilayer structures that have a PS base layer and a PtBA top layer. The tert-butyl acrylate groups of the PtBA layer of 0.9 nm were converted to carboxylic acid groups with trifluoroacetic acid for respective esterification with the two hydroxy-containing QASs. It was observed that the fluorinated and nonfluorinated surfaces fabricated at the maximum comparable esterification yield of 63.5% fully eradicated ∼104 CFU of Staphylococcus aureus and Escherichia coli in 120 and 150 min, respectively, indicating that the fluorocarbon chain is more biocidal through better interpenetration into bacterial membranes. Immobilization of a functionality on top surface provides a universal strategy to study its structural contribution to activity without interference of the concentration distribution.