In this work, structural stability and thermal transformation of Pt-Sn bimetallic nano clusters are studied by molecular dynamics simulations, combined with the modified embedded atom method. For a more accurate description of the interatomic interactions, new Modified Embedded Atom Method alloying parameters for Pt-Sn are derived based on ab initio density functional theory calculations. The calculated Gibbs free energies of formation show that all kinds of structures are energetically favorable and the most stable structure is solid solution cluster, and then the core/shell, and eutectic-like cluster. For whatever compositions the eutectic-like clusters must transform into one pure Sn cluster and one Pt core/Sn shell cluster up to certain temperature during heating process, the Sn coverage on Pt core is dependent on its composition. For solid solution and Pt core/Sn shell or Sn core/Pt shell, once the structure forms, it can keep basically unchanged from the point of view of elemental distribution. Surface segregation is not apparent observed.