Poly(ethylene oxide) (PEO)-based composite electrolytes (PCEs) are considered as promising candidates for next-generation lithium-metal batteries (LMBs) due to their high safety, easy fabrication, and good electrochemical stability. Here, we utilize operando grazing-incidence small-angle and wide-angle X-ray scattering to probe the correlation of electrochemically induced changes and the buried morphology and crystalline structure of the PCE. Results show that the two irreversible reactions, PEO-Li+ reduction and TFSI- decomposition, cause changes in the crystalline structure, array orientation, and morphology of the PCE. In addition, the reversible Li plating/stripping process alters the inner morphology, especially the PEO-LiTFSI domain radius and distance between PEO-LiTFSI domains, rather than causing crystalline structure and orientation changes. This work provides a new path to monitor a working battery in real time and to a detailed understanding of the Li+ diffusion mechanism, which is essential for developing highly transferable and interface-stable PCE-based LMBs.