This study employs theories involving saturated vapor pressure, separation coefficient, and vapor–liquid equilibrium composition to investigate the feasibility of using vacuum distillation to separate phosphorus and arsenic. Ab initio molecular dynamics simulations are used to analyze the structure, stability, and dynamics of AsnPm (m + n ≤ 8) clusters, assessing their impact on removing arsenic during the vacuum distillation of industrial yellow phosphorus. Theoretical calculations indicate that vacuum distillation is an effective method for removing arsenic from industrial yellow phosphorus. Throughout the vacuum distillation process, clusters like AsP, AsP2, AsP3, and others are prone to diffuse into the gas phase and remain stable, affecting the efficiency of arsenic removal. The collected red phosphorus shows a reduced arsenic content from 136 mg/kg to 1.09 mg/kg, confirming the feasibility of using vacuum distillation to eliminate arsenic from industrial yellow phosphorus and convert it into stable red phosphorus.