During the past two decades, it has become clear that structural defects can greatly alter the behavior of nanoscale materials. With increased use of nanomaterials in the electrode architecture of Li-ion batteries, one should take into account how such defects can influence the electrochemical response of battery electrodes. In spite of this need, our fundamental understanding about the kinetics of lithium ions at microstructural defects is at its infancy. Here, we report, for the first time, the lithiation behavior of the individual SnO2 nanowires containing twin boundary (TB). Comparing with the single crystal SnO2 nanowire, in which the lithium ions preferred to diffusion along the  direction, our in situ TEM study indicates that the lithium transport pathway will totally change when the TB exists inside the SnO2 nanowires. Direct atomic-scale imaging of the initial lithiation stage of the TB-SnO2 nanowire and the DFT simulations prove that the lithium ions prefer to intercalate in the vicinity of the TB, which acts as a conduit for lithium ion diffusion inside the nanowires. Our results should lead to working out the great impact of interfaces on mass transfer, transport and storage and guide the development of high performance electrochemical devices that rely on ion transport by microstructure engineering.