A systematic study on Ln2Si6q (Ln = Sm, Eu, Yb; q = 0, −1) clusters has been performed by density functional theory (DFT). Global minimum searches reveal that the two lanthanide atoms prefer to absorb on the surface of parent silicon-based clusters. Natural population analysis (NPA) is utilized to investigate the electronic and magnetic properties of Ln2Si6q, the electrons always transfer from the lanthanide atoms to parent silicon atoms. Most interestingly, the DFT calculations demonstrate that the magnetic moments of the doped rare earth atoms remain largely localized (13μB for Sm2Si6−/ Eu2Si6−, 12μB for Sm2Si6 and 14μB for Eu2Si6), and the atomic-like magnetism is maintained in the doped cluster. Combined with average binding energy, dissociation energy and HOMO-LUMO gap, Sm2Si6 is probed to the most stable cluster. The current work shows that lanthanide diatom doped silicon-based clusters could have potential utility in new rare earth nanomaterials with tunable magnetic properties.