The MoSi2 nanocrystal was prepared by mechanical alloying (MA) large particle-sized starting powders, in which the milling time is much longer than usual MA time. It was found that the Mo-Si powder mixture mixed at stoichiometry proportion forms α-MoSi2 and β-MoSi2 in the MDR mode rather than pure α-MoSi2 in the SHS mode. The grain size of MoSi2, calculated using Scherrer′s formula, is 18nm when milled for 96h, and decreases to 12nm when further milling to 144 h. This is because that the milling balls provide enough energy to refine most of the rough crystal grain. The average grain size increased to 15nm when milled for 192 h, which indicates that further expand time could not refine the crystal grain while cause the growth of a part of the crystal grain. The particle size of MoSi2 is about 0.5μm when milled for 96 h and the agglomerating phenomenon is severe. The particle size of MoSi2 decreases to 0.4μm and releases the agglomerating phenomenon with the milling time for 144 h.