The performance of alkali-metal-ion batteries largely depends on the migration behavior of alkali metal ions in the electrodes. Probing the atomic structure of the reaction interface and the dynamic process during ion transport in the electrodes will help better understand the underlying electrochemical mechanisms and inspire rational electrode designs. In this study, by combining in situ transmission electron microscopy (TEM) and aberration-corrected scanning TEM (STEM), we track the reversible lithium ion transport in MoS2 nanostructures to reveal the atomic structure and dynamic behaviors of the reaction interface. We find that lithium ions insertion triggers complex phase transformations. Three different phases co-exist at the interface: a pristine 2H phase, a 1T phase with a shrank lattice constant of − 3.3% ( ± 2.3%), and a distorted 1T phase (called 1Tˊ phase) with an expanded lattice constant of 5.5% ( ± 2.5%). The atomically resolved Z-contrast image shows that the expanded 1Tˊ phase has distorted Mo arrangements. Furthermore, the lithium ions migration causes defects at the reaction front, and the diffusion on the surface is faster than that inside, forming a core-shell structure at the reaction interface. The diffusivity of lithium ions is directly measured to be ~1000–30,000 nm2/s, which is significantly higher than that of sodium insertion (~10–20 nm2/s). The atomic-scale observations of lithium-ion-migration-induced complex structural evolutions would help understand the properties of MoS2 nanostructures and shed light on the design of alkali-metal-ion batteries with general transition-metal dichalcogenide electrodes.