Molybdenum disulfide (MoS2) is a promising high‐capacity anode for lithium‐ion batteries. However, the conversion reaction mechanism of MoS2 (the delithiation pathway in particular) has been controversial, which limits the rational optimization of its electrochemical performance. The main challenge is how to precisely identify the amorphous nanomaterials generated during lithiation/delithiation. Here, the structural evolutions of MoS2 during lithiation/delithiation are systematically investigated using synchrotron X‐ray absorption spectroscopy at Mo K‐edge and S K‐edge and Raman spectroscopy. It is revealed that amorphous MoS2 nanograins rather than sulfur as previously suggested, are formed after delithiation, and that the fully lithiated MoS2 electrode contains additional Mo‐S related phases besides the known Mo and Li2S. Density functional theory simulations suggest that the Mo nanoparticles formed during lithiation are very reactive with Li2S, thus enabling the regeneration of MoS2 upon delithiation. These findings deepen the understanding of the lithiation/delithiation mechanism of MoS2, which will pave the way for the rational design of advanced MoS2‐based electrodes.