The local structure and dynamics of impurities Fe, Al and Mn in beryllium were investigated on an atomic scale using ab initio molecular dynamics and statistical physics methods. The analysis of the radial distribution function centered on impurity atoms shows that the density of beryllium atoms around Fe and Mn is 8.4% and 8.6% higher than that around Al, respectively. The statistics of the measure square displacement of impurity atoms show that the diffusion coefficients of Al atoms are 114% and 133% larger than that of Fe and Mn atoms in the melt beryllium, respectively. Statistical analysis of velocity autocorrelation function of impurity atom shows that Fe and Mn atoms collide strongly with beryllium atoms in the first coordination layer, indicating that they are tightly surrounded and bound by the surrounding beryllium atoms in the central position, while the beryllium atoms around Al are loosely arranged and have weak binding forces with Al. The analysis of the activity coefficients of the impurities shows that when Fe or Mn enters the melt beryllium, it reduces the free energy of the system, whereas when Al enters, it increases the system energy. In summary, the interatomic force of BeAl is weak, so they do not form intermetallic compounds, and Al diffuses quickly in beryllium. While BeFe and BeMn have strong interatomic forces, and tend to form more BeFe and BeMn bonds to reduce the free energy of the system, so Fe and Mn diffuse slowly in beryllium. Ab initio molecular dynamics can be used to forecast the best experimental temperature for the vacuum distillation of beryllium.