A change in the microstructure of Ti-Si alloys synthesized by high-energy mechanical milling through post-annealing significantly enhances their electrochemical performances as anode materials for lithium-ion batteries (LIBs). The microstructures of ball-milled and post-annealed powders are investigated using high-resolution transmission electron microscopy (HR-TEM). The Si phase is uniformly distributed on the silicide (TiSi2) matrix. The individual Si domains of the mechanical alloying (MA) sample consist of amorphous and crystalline regions with a diffuse interface between the two phases. When MA powder is annealed at 600 °C, the Si phase has a well-developed nanocrystalline microstructure: a multi-grain structure with random orientation of nanometric crystal domains. Annealing at 600 °C causes a significant improvement in electrochemical performance parameters like cycling stability and rate capability. However, when annealed at 800 °C, the electrochemical performances deteriorate due to an increase in the size of Si domains.