Thin ZnSnO films with different thickness deposited on Si substrates by aerosol spray pyrolysis were investigated by scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDX), X-ray diffraction (XRD), atomic force microscopy (AFM) and light microscopy (LM) using depth-sensitive nanoindentation with Berkovich indenter. The values of the Young modulus (E), nanohardness (H), and plasticity index (H/E) of the prepared films were determined according to the Oliver-Pharr method in the diapason of the applied loads of 30–300 mN. The main factors contributing to the nanomechanical properties of film-substrate structures were identified, and the deformation mechanisms of the ZnSnO/Si coated system (CS) under nanoindentation have been revealed.