AuNi alloy nanoparticles were successfully immobilized to MIL-101 with size and location control for the first time by double solvents method (DSM) combined with a liquid-phase concentration-controlled reduction strategy. When an overwhelming reduction approach was employed, the uniform 3D distribution of the ultrafine AuNi nanoparticles (NPs) encapsulated in the pores of MIL-101 was achieved, as demonstrated by TEM and electron tomographic measurements, which brings light to new opportunities in the fabrication of ultrafine non-noble metal-based NPs throughout the interior pores of MOFs. The ultrafine AuNi alloy NPs inside the mesoporous MIL-101 exerted exceedingly high activity for hydrogen generation from the catalytic hydrolysis of ammonia borane.