Diffusion bonding of refractory Nb–Si-based alloy was performed with Ni/Al and Ti/Al nanolayers under the condition of 1473 K/30 MPa/60 min. The NbSS/Nb5Si3 in situ composite with the nominal composition of Nb–22Ti–16Si–3Cr–3Al–2Hf was used as the parent material. The joint microstructures were examined by using a scanning electron microscope equipped with an X-ray energy dispersive spectrometer. Shear test was conducted for the bonded joints at room temperature. Within the joint bonded with Ni/Al multilayer, element diffusion occurred between the base metal and the nanolayer, with the reaction products of AlNb2 + Ni3Al, NiAl and AlNi2Ti phases. The average shear strength was 182 MPa. While using Ti/Al multilayer, the interface mainly consisted of TiAl, (Ti,Nb)Al and (Ti,Nb)2Al phases, and the corresponding joints exhibited an increased strength of 228 MPa. In this case, the fracture mainly took place in the TiAl phase and presented a typical brittle characteristic.