The detection sensitivity of synchrotron-based X-ray techniques has been largely improved due to the ever-increasing source brightness, which has significantly advanced ex situ and in situ research for energy materials such as lithium-ion batteries. However, the strong beam–material interaction arising from the high beam flux can substantially modify the material structure. The beam-induced parasitic effect inevitably interferes with the intrinsic material property, making the interpretation of the experimental results difficult and requiring comprehensive assessments. Here, we present a quantitative study of the beam effect on an electrode material Ag2VO2PO4 using four different X-ray characterization methods with different radiation dose rates. The material system exhibits interesting and reversible radiation-induced thermal and chemical reactions, further evaluated under electron microscopy to illustrate the underlying mechanism. The work will provide a guideline for using synchrotron X-rays to distinguish the intrinsic behavior from extrinsic structure change of materials induced by X-rays.