Dual-phase metal materials can usually take into account the advantages of both phases, but the heterogeneity of dual-phase properties will cause flow instability. Therefore, it is difficult to further improve the microstructure and properties of Nb–Si–Ti based alloys containing ductile Nbss and hard silicides through hot working. Here, we propose a method for interface modification by precipitating an intermediate phase and forming a core-shell-like structure with silicides. A novel near core-shell structure (β-Nb5Si3/Nb4FeSi) is obtained in Nb–Si–Ti based alloy by deep cryogenic quenching and annealing. The precipitation of Nb4FeSi is closely related to stacking faults, where high-density stacking faults can develop into the nanotwins during annealing at 1200 °C. In addition, two types of nanoprecipitation behaviors are observed in the Nbss and β-Nb5Si3. The nanoscale plate-like δ-Nb11Si4 is precipitated along the [100]Nbss and [010]Nbss in the Nbss matrix, while the precipitation of granular Nb4FeSi from β-Nb5Si3 satisfies (1‾10)β//(01‾0)Nb4FeSi. In addition to the twinning induced plasticity of Nb4FeSi (shell), a phase transformation from β-Nb5Si3 to α-Nb5Si3 and Nbss that occurs within the core-shell structure is beneficial for the hot forming of the alloy.