In this paper, 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 showed that the density of beryllium atoms around Fe and Mn is 8.4% and 8.6% higher than that of beryllium around Al, respectively. The statistics of the measure square displacement of impurity atoms showed that the diffusion coefficients of Al atoms are 114% and 133% larger than those of Fe and Mn atoms in the melt beryllium, respectively. Statistical analysis of velocity autocorrelation function of impurity atom showed that Fe and Mn atoms collided strongly with beryllium atoms in the first coordination layer, indicating that they were 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 showed that when Fe or Mn entered the melt beryllium, it reduced the free energy of the system, while when Al entered, it increased 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, BeMn have strong interatomic forces, and tend to form more BeFe and BeMn bonds to reduce the free energy of the system, thus Fe, Mn diffuse slowly in beryllium. Ab initio molecular dynamics can be used to forecast the best experimental temperature for the vacuum distillation of beryllium. It provides an efficient and convenient means to guide the purification of beryllium.