Hydrophobic coatings for practical applications demand good durability of hydrophobicity and excellent adhesion. Therefore, the preparation of crosslinked crystalline polymers with perfluoroalkyl side-chains and long alkyl side-chains were proposed. In this paper, the influence of the crosslinking on the crystallization of fluorinated acrylate copolymers was investigated through experimental and molecular dynamic simulation results. According to the FT-IR spectroscopy, XRD data and DSC curves, P(SA-co-HEMA-co-FOEMA) was amorphous, while P(SA-co-FOEMA) and the cured resin formed crystalline polymers with hexagonal packing of alkyl side-chains, and the degree of crystallinity in the cured resin is larger than that in P(SA-co-FOEMA). These phenomenons were further interpreted through the snapshots of the equilibrated systems, the radial distribution function, and the concentration profiles. Intramolecular hydrogen bonds and arrangement of main-chains, corresponding to the embedding of N3300, were considered to contribute to these phenomenons. These findings could be expanded to other comb-shape crystalline polymers for preparing functional surfaces and smart materials.