In this study, a novel two-stage vacuum distillation method was proposed to refine crude indium to prepare refined indium. Low-temperature distillation (1223K, holding time of 3h) and high-temperature distillation (1473K, holding time of 5h) were conducted under a system pressure of 7 × 10−3Pa to successfully purify crude indium (99 wt%) to refined indium (99.995 wt%). This strategy can replace the traditional electrolytic process for the clean production of refined indium and achieve the goals of environmental protection. The vapor-liquid equilibrium (VLE) values of indium-based binary alloys were calculated using the molecular interaction volume model (MIVM), and a VLE phase diagram was drawn. Optimal temperatures of 1173K for low-temperature and 1373K for high-temperature distillation were determined based on the VLE phase diagram, and good purification was achieved. Moreover, this study reveals the migration distribution pattern of typical impurity elements (e.g., Tl and Sn) in crude indium in the low and high-temperature distillation sections, further improving the refining effect. Notably, the combination of MIVM simulations and experiments can obtain optimal experimental parameters for segmental vacuum distillation and further help to avoid the waste of raw materials and energy caused by pre-experiments, realizing the clean and efficient production of refined indium.