A good understanding of the surface hydrophobicity of fluorinated materials is useful for their application as coating materials. The present study investigates the surface hydrophobicity of perfluoroalkyl acrylate (PFA) thin films using molecular dynamics simulations. Surface hydrophobicity is characterized by examining the contact angle of a water droplet on PFA surfaces and the cavity formation free energy in the vicinity of the surface. It is found that the calculated microscopic contact angles are in good agreement with the experimental results and partially capture the difference in the hydrophobicity of the surface arising from the variation of packing density and side chain length of PFA. The variations of cavity formation free energy in the vicinity of the surface elucidate that the surface hydrophobicity is mainly governed by the packing density rather than the chain length of PFA. The hydrophobicity generally increases with decreasing the packing density to some extent and then turns to decrease as further reducing the packing density. At higher packing density, the surface hydrophobicity slightly decreases with increasing the chain length, while at the lower packing density, the surface hydrophobicity is increased when chain length of PFA is longer than six carbons. Furthermore, we found that the influence of packing density on the surface hydrophobicity is directly related to the variation of the surface roughness and chain flexibility, that is, the surface hydrophobicity increases with increase in the surface roughness, while the chain flexibility plays a secondary role in the enhancement by affecting the stability of water staying near the interface. The study provides a significant insight into the local hydrophobicity and microscopic structure of the PFA surfaces, which would be useful for the application of surface modification.