MXenes, layered transition metal carbides/nitrides, have already received considerable attention in various research areas including but not limited to energy storage/conversion and photo/electrocatalysis. In fact, the intrinsic property of MXenes is highly tunable by controlling the surface terminations and interlayer spacing. Moreover, synchrotron radiation X-ray characterizations have shown high potential for exploring the causal relationship between the properties and structure of MXenes. Particularly, operando X-ray measurements could provide useful insight for better understanding the dynamic process of MXene-based energy materials. In this review, a comprehensive summary of recent studies on surface controlling, interlayer engineering, and the synchrotron-based characterizations of MXenes is presented. The outlook of MXenes and applications of advanced X-ray characterizations are also discussed.