In situ low-voltage transmission electron microscopy (TEM) was performed to study the evolution of small Pt clusters on suspended graphene. Pt clusters, trapped by the edge of holes, generally take a stable shape of truncated octahedron for sizes ranging from sub-1 to ∼5 nm. The interaction to the graphene dots takes in charge when they form composite nanostructures embedded in graphene. The Pt clusters are slowly flattened due to hole enlargement under electron irradiation. The planar structure is maintained by the peripheral Pt-C bonds and instantly collapses into a three-dimensional (3D) cluster if one side is detached from the edge. Based on the heat transfer model, the thermal effect can be excluded under the experimental condition. Atomistic evolution can be attributed to the electron irradiation. Molecular dynamics simulations revealed that the evolution kinetics was found to be dominated by the surface diffusion (characterized by the migration barrier Em), the temperature (the thermal activation energy ∼5kBT), and the scattering from electrons (the maximum transferred energy Emax). The corresponding energies are comparable for the Pt cluster system, leading to similar evolution behaviors. A different scenario in graphene systems is due to the large difference in agitations, i.e., Emax ≫ Em ∼ 5kBT at 3000 K. This unique behavior comes from TEM observation, implying that electron beam irradiation can be utilized as a unique tool in shaping carbon nanostructures.