Abstract The clustering processes of Fe atoms in liquid Li at different temperatures and the effect from the Fe clusters on the viscosity of liquid Li are investigated using molecular dynamics simulation combined with the embedded atom method. The clustering processes are vividly captured by the microstructure evolution snapshots and the details are uncovered by the cluster analysis results. The cluster analysis results indicate the higher the temperature the faster the clustering process, and the temperature-dependent mixing enthalpy of Li–Fe (solute) dilute solution also suggests that high temperature is beneficial to Fe atoms’ clustering. In addition, our results show that the Fe clusters can dramatically increase the viscosity of liquid Li by lowering the diffusivity of the Li atoms around it, and the larger the clusters the larger the viscosity increment.