Separation and recovery of molybdenum (Mo) with high concentrations from spent catalysts is a strategy for avoiding the environmental footprint by metal mining and the disposal of hazardous wastes, while alleviating resource shortage. In this paper, a method for constructing a binary (SiO 2 −Na 2 O)/ternary (SiO 2 − Na 2 O−B 2 O 3 ) glass phase extraction (GPE) system to selectively extract the impurity metal ions from spent catalysts as well as simultaneously separate and recover Mo is presented. Based on experimental studies and classical molecular dynamics simulations, compared with the binary glass network, 99.4% of Al 3+ and Ni 2+ in spent catalysts were extracted in a more stable tetra-coordinated form at a lower melting temperature (1200 °C) by the ternary GPE system introducing B 2 O 3 , accompanied by Na 2 MoO 4 precipitated as the recovery product. The recovery efficiency of Mo was 98.1%, realizing an efficient separation and short-process recovery. Moreover, the separation of Na 2 MoO 4 melt and glassy liquid during the melting process was visually observed online. Therefore, this approach of constructing glass GPE systems for the one-step separation of metals during the melting process is expected to contribute to the sustainable supply of critical metals.