Nanostructured C-Ag thin films of 200 nm thickness were successfully synthesized by the Thermionic Vacuum Arc (TVA) method. The influence of different substrates (glass, silicon wafers, and stainless steel) on the microstructure, morphology, and mechanical properties of nanostructured C-Ag thin films was characterized by High-Resolution Transmission Electron Microscopy (HRTEM), Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), and TI 950 (Hysitron) nanoindenter equipped with Berkovich indenter, respectively. The film’s hardness deposited on glass (HC-Ag/Gl = 1.8 GPa) was slightly lower than in the case of the C-Ag film deposited on a silicon substrate (HC-Ag/Si = 2.2 GPa). Also the apparent elastic modulus Eeff was lower for C-Ag/Gl sample (Eeff = 100 GPa) than for C-Ag/Si (Eeff = 170 GPa), while the values for average roughness are Ra=2.9 nm (C-Ag/Si) and Ra=10.6 (C-Ag/Gl). Using the modulus mapping mode, spontaneous and indentation-induced aggregation of the silver nanoparticles was observed for both C-Ag/Gl and C-Ag/Si samples. The nanocomposite C-Ag film exhibited not only higher hardness and effective elastic modulus, but also a higher fracture resistance toughness to the silicon substrate compared to the glass substrate.