Melt-spun Si based alloy materials have gained much attention as high capacity anode materials for lithium-ion batteries because of their high capacity and relatively low production cost. However, their long-term cycle performance should be further improved for the commercial success. Herein, it is demonstrated that the electrochemical performances of Si/TiFeSi2 active-inactive nanocomposite anode material could be further improved by the microstructural modification using its mechanical deformation. With the help of high-energy mechanical milling, the microstructural tuned Si/TiFeSi2 nanocomposite material showed a reversible capacity of more than 1000mAhg−1 with stable capacity retention up to 100 cycles. Ex situ X-ray diffraction analysis coupled with potentiostatic intermittent titration technique revealed that refining the sizes of the active Si and inactive TiFeSi2 limited the lithiation of Si phase to Li21Si8 and this suppressed lithiation led to less volume changes of the electrodes and the improvement of the mechanical integrity of Si/TiFeSi2 nanocomposite material.