Fluoropolymer brushes are widely used to prevent nonspecific adsorption of commercial polymeric or biological materials due to their strongly hydrophobic character. Herein, a series of fluoropolymer brushes with different compositions, thicknesses and molecular architectures was prepared via surface-initiated atom transfer radical polymerization (ATRP). Subsequently, the antifouling properties of these fluoropolymer brushes against organic polymers were studied in detail using X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) measurements and polystyrene as a representative fouling polymer. Among all of the molecular architectures studied, homopolymerized methacrylate-based fluoropolymer brushes (PMAF17) show the best antifouling properties. Annealing the fluoropolymer brushes improves the antifouling property dramatically due to the reregulated surface composition. These fluoropolymer brushes can be combined with, e.g., micro- and nanostructuring and other advanced materials properties to yield even better long-term antifouling behavior under harsh environments.