The influence of the surface structure and vibration mode on the resistivity of Cu films and the corresponding size effect are investigated. The temperature dependent conductivities of the films with different surface morphologies are calculated by the algorithm based upon the tight-binding linear muffin-tin orbital method and the Greens function technique. The thermal effect is introduced by setting the atomic displacements according to the Gaussian distribution with the mean-square amplitude estimated by the Debye model. The result shows that the surface atomic vibration contributes significantly to the resistivity of the systems. Comparing the conductivities for three different vibration modes, it is suggested that freezing the surface vibration is necessary for practical applications to reduce the resistivity induced by the surface electron-phonon scattering.