Inorganic thin films on polymer substrates have enhanced functionalities in electronic, packaging, and energy conservation applications. Nevertheless, establishing a robust interfacial bond between the thin film and substrate remains a significant challenge. Polymer substrates inherently possess unique properties, and this review compares the changes observed in aliphatic and aromatic polymers after ion and plasma treatments. The analysis also reveals various factors from the substrate that can influence by the treatments. Additionally, process parameters of the treatment, such as process gas, energy of ion and plasma species, and treatment duration are critical to determine effects of treatment to the polymer substrates. Factors affecting interfacial bonding between inorganic thin film and polymer substrate and residual stress generated in the thin film-substrate system have been systematically reviewed. Furthermore, a significant focus of this review is placed on the impact of weathering effects, such as sunlight with UV irradiation, humidity, and temperature, on the durability of thin film-polymer substrate system and typical thin film adhesion quality characterization techniques.