AbstractDue to the long‐range atomic disorder and more active sites, amorphous MXenes with better chemical reactivity and electrical conductivity, have attracted wide attention in energy storage devices. However, to reach the practical applications of MXenes, investigations into the best structure of the amorphous layer are essential. Here, the structure evolution of MXenes induced from ammonium persulfate is explored via synchrotron radiation X‐ray absorption spectroscopy. Then, a kind of oxygen‐poor amorphous heterojunction Nb2CTx MXene (a‐Nb2CTx) is designed. Benefitting from the oxygen‐poor amorphous heterojunction, the a‐Nb2CTx electrode exhibits excellent Li+ storage performance with a high discharge specific capacity of 382 mAh g−1 at 0.1 A g−1 and a long cycling stability of 300 mAh g−1 at 1.0 A g−1 after 800 cycles. Operando synchrotron X‐ray diffraction results reveal that oxygen‐poor amorphous heterojunction stabilizes Nb2CTx MXene from undergoing structural changes during cycling. This work provides new insights into the rational design of novel amorphous MXenes, which is of great significance for the development of MXenes and their applications in high‐performance energy storage systems.