This review provides detailed fundamental principles of X-ray-based characterization methods, i.e., X-ray photoelectron spectroscopy, energy-dispersive X-ray spectroscopy, and near-edge X-ray absorption fine structure, and the development of different techniques based on the principles to gain deeper understandings of chemical structures in polymeric materials. Qualitative and quantitative analyses enable obtaining chemical compositions including the relative and absolute concentrations of specific elements and chemical bonds near the surface of or deep inside the material of interest. More importantly, these techniques help us to access the interface of a polymer and a solid material at a molecular level in a polymer nanocomposite. The collective interpretation of all this information leads us to a better understanding of why specific material properties can be modulated in composite geometry. Finally, we will highlight the impacts of the use of these spectroscopic methods in recent advances in polymer nanocomposite materials for various nano- and bio-applications.