In this study, hydrophobic plasma polymer films were prepared from perfluorohexane with saturated linear structure and octafluorotoluene with a cyclic unsaturated structure. Hydrophilic plasma polymer film was prepared from acrylic acid with an unsaturated linear structure. The film deposition rates were compared through in-situ laser interferometer measurement and correlated them with the precursor structure and the deposition parameters. The chemical structure and the surface energy of the films were also investigated with FTIR and contact angle measurement. The results showed that the deposition rate increased with the discharge power. otherwise, the deposition rate relied on the structure of the precursors to a large extent. The deposition rate of octafluorotoluene is 7 times the deposition rate of perfluorohexane and 5 times the deposition rate of acrylic acid at the same deposition parameters. So a high deposition rate could be obtained for the precursors with cyclic and unsaturated structures. For the pulse discharge of acrylic acid, there existed a maximum deposition rate for a certain pulse frequency. But it was found that the pulse frequency had greater effects on the structure of the plasma films than on the deposition rate. As the pulse frequency decreased, more CHO and O-C=O groups were found in the deposited film of acrylic acid. And the pulse discharge at low power could keep more aromatic ring in octafluorotoluene plasma film than continuous discharge at high power. This explained the phenomenon that the surface energy of octafluorotoluene plasma film deposited by the low power pulse discharge was lower than that of the film deposited by the high power continuous discharge and showed to be more hydrophobic.