This study investigates the mechanochemical synthesis and microstructural evolution of Ti60Al40+B3(Y2O3)5 powders subjected to high-energy mechanical alloying for 12, 24, and 48 hours. CALPHAD-based thermodynamic simulations predicted multiphase stability regions and quantified the distribution of Ti, Al, B, and Y in equilibrium phases, including the activities of each constituent, establishing a theoretical baseline for comparison with experimentally induced metastable states. Mechanical alloying produced progressive grain refinement, with median grain sizes decreasing from 0.07 μm (12 h) to 0.04 μm (48 h), consistent with severe plastic deformation and defect accumulation. Crystallite size analysis indicated a significant reduction from 18.054 nm at 12 hours to 7.042 nm at 48 hours, reflecting enhanced lattice strain and grain refinement induced by prolonged milling. SEM and EDS analyses confirmed improved homogenisation, enhanced Ti–Al mixing, and the evolution from discrete elemental regions to a chemically uniform nanostructure. X-ray diffraction revealed a clear reaction pathway characteristic of a fully reactive MA system. At 12 h, only elemental α-Ti, fcc-Al, and residual Y2O3 were detected, reflecting limited reaction. After 24 h, the emergence of TiAl, Ti3Al, and TiB2 peaks signalled the onset of intermetallic and boride formation. By 48 h, the powders fully transformed into a nanocrystalline TiAl/Ti3Al matrix reinforced by TiB2, while Y2O3 became largely amorphous and incorporated into a disordered Y–Ti–O phase. The complete disappearance of Ti and Al reflections confirms full consumption of reactants, consistent with a fully reactive mechanochemical process. It was observed that extended milling produced a highly refined, chemically homogeneous nanocomposite consisting of TiAl/Ti3Al intermetallics, TiB2 ceramic reinforcements, and an amorphous Y–Ti–O dispersoid phase. These findings provide insight into phase evolution mechanisms and offer valuable guidance for optimizing MA parameters for Ti–Al–B–Y2O3 powder systems aimed at high-performance structural applications.