The lying-down and standing-up CuPc and F₁₆CuPc films on HOPG (highly ordered pyrolytic graphite) and C8-SAM/Au(111) (octane-1-thiol terminated Au(111)) substrates are investigated by using a hybrid strategy combing the molecular dynamic (MD) simulations with density functional theory (DFT) calculations, in order to understand the influence of packing orientation on charge carrier mobilities. On the basis of the periodic slab model and consistent-valence force field, MD simulations show the populations of various packing configurations and radial distribution of intermolecular distance in the films at room temperature. It is also demonstrated that the external electric field (parallel or perpendicular to the substrate) perturbs the intermolecular distances in CuPc and F₁₆CuPc films, especially for the slipped edge-to-face stackings. DFT calculations are then used to evaluate two key charge-transfer parameters, reorganization energy and transfer integral. An electrostatics embedding model is employed to approximately consider the external electrostatics contributions to reorganization energy. The thermal-averaged mobility is consequently estimated by taking account of both electronic structures of charge-hopping pairs and dynamic fluctuations in film morphologies under various experimental conditions. It is found that CuPc has smaller reorganization energy and larger hole (electron) mobilities than F₁₆CuPc. Under the external electric field of 10⁴–10⁷ V cm⁻¹, both hole and electron mobilities of CuPc and F₁₆CuPc films would decrease to 1–3 orders of magnitude. CuPc (F₁₆CuPc) films show substantial orientation dependence of mobilities on the ratio of standing-up versus lying-down orientations falling in the range of 10–1000.