Lewis acidic molten salt method is a promising synthesis strategy for achieving MXenes with controllable surface termination from numerous MAX materials. Understanding the phase evolution chemistry during etching and post-processing is highly desirable but remains a key challenge due to the lack of suitable in-situ characterizations and the complexity of the reaction process. Herein, we introduce an operando synchrotron radiation X-ray diffraction (SRXRD) technique to unveil the phase evolution process of Nb2GaC MAX under a molten-salt ambient, proposing a controllable synthesis to achieve optimal etching through precise temperature and time adjustment. Subsequently, the phase structure of Nb2CTx MXenes is successfully tailored from hexagonal to amorphous by time-dependent persulfate oxidation. The resulting amorphous Nb2CTx with a well-patterned morphology and numerous chloride terminations exhibits highly improved specific capacity, rate capability, and long cycling for Li+ storage with a Cl-containing surface protective film. Addressing the time-related phase evolution during the entire molten salt strategy provides new insights into achieving higher efficiency and controllability in preparing MXenes and shows great potential in high-performance energy storage systems based on MXenes.