Proton conductive copolymers of 1H,1H,2H,2H-perfluorodecyl acrylate (PFDA) and methacrylic acid MAA have been synthesized by initiated chemical vapor deposition (iCVD). Detailed insights into the copolymers' molecular organization were gained through an X-ray-based investigation to serve as a starting point for systematic studies on the relation among proton conductivity and polymer structure. The method of copolymerization, iCVD, facilitated the tuning of the ratio between acidic COOH groups, coming from MAA, and the hydrophobic matrix from the PFDA components. It was demonstrated that the copolymers crystallize into a bilayer structure, formed by the perfluorinated pendant chains of PFDA, perpendicular to the substrate surface. The MAA molecules form COOH-enriched regions among the bilayers parallel to the substrate surface which can act as ionic channels for proton conduction when the acid groups are deprotonated. The interplanar distance between the bilayer lamellar structures increases by the presence of MAA units from 3.19 to 3.56 nm for the MAA PFDA copolymer with 41% MAA, therefore yielding to 0.4 nm wide channels. Proton conductivities as high as 55 mS/cm have been achieved for copolymers with 41% MAA fraction. Such ordered, layered nanostructures were never shown before for copolymers deposited from the vapor phase, and their anisotropy can be of inspiration for many applications beyond proton conduction. Moreover, the one-step copolymerization process has the potential to manufacture inexpensive, high quality membranes for proton exchange membrane fuel cells.