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Abstract The processes of phase separation and surface segregation which take place during two-component nanocomposite Metal:Carbon thin film growth are analyzed. The mathematical model is proposed which includes the processes of adsorption, phase separation, surface segregation, surface and bulk diffusion. The process of phase separation is described using Cahn-Hilliard equation and the process of surface segregation is described by Gibbsian segregation model. Diffusion in growing film is allowed to occur in a layer of an arbitrary thickness near the surface. The formations of metal clusters, columns or surface layer in matrixes of carbon are shown by the numerical simulations depending on thin film growth conditions. The influence of film composition and deposition temperature on film morphology is analyzed by the presented simulations. The simulation results are compared with experimental data taken from literature where C:Ni thin films were grown at different contents of Ni and substrate temperatures. The simulation results are in a good agreement with the corresponding experimental data. Graphical abstract Unlabelled Image Highlights • A model for phase separation and surface segregation during film growth is proposed. • Modeling results are consistent with experimental results of the C:Ni thin films. • Depending on conditions, model results exhibit layered, columnar, granular patterns. [ABSTRACT FROM AUTHOR]