Carbon based materials have attracted much for its unique surface microstructure and nanomechanical properties among researchers. In this study, the influence of microstructure on the nanomechanical properties of thin carbon based films was studied in detail. For which amorphous Carbon nitride (a-CN) and Titanium incorporated amorphous Carbon nitride (Ti/a-CN) thin films were prepared with a thickness of less than 100 nm using hybrid ion beam deposition technique. The incorporation of Ti into the a-CN matrix greatly modified the sp3/sp2 hybridized bonding ratio and it is reflected in the mechanical hardness of Ti/a-CN thin film. Most of the incorporated Ti reacts with carbon and nitrogen to form TiN and TiCN phases respectively. On the other hand, owing to the usage of energetic ion bombardment and the presence of TiN/TiCN phases in the carbon nitride matrix, the Ti/a-CN nanocomposite film shows improved adhesion strength compared to that of pure a-CN film. Overall the presence of hard metallic phase in the amorphous carbon network alters the microstructure and improves the adhesion strength of a-CN films suitable for protective coating applications.