The nano-hardness and elastic modulus on (001), (100), and (110) planes of Nbss and α-Nb5Si3 phase in Nb-Si alloys were investigated by nanoindentation. Electron backscatter diffraction (EBSD) and scanning electron microscopy (SEM) were performed to research the surface orientation and morphology of the enhancing deformation fields around the indents. The orientation dependence of microcosmic fracture toughness in Nb-Si alloys was predicted by the nano-hardness and elastic modulus of the individual phase. A simple phase boundary crystallographic model of (110) Nbss // (110) α-Nb5Si3 between Nbss and α-Nb5Si3 phases was established by EBSD analysis. The Easy-slip model was adopted to explain nanoindentation-induced deformation mechanisms of Nbss, which point to the activation of slip plane in the maximum Schmidt factor.