γ-TiAl alloy has a range of application in the aerospace and automotive fields because of its excellent properties. During the process of powder metallurgy, thermal stability and microstructure change in the sintering process of TiAl alloy nanoparticles have an important influence on the microstructure and properties of products. In this present study, molecular dynamics calculations are performed to study the atom packings of the nanoparticles during heating and coalescence within the framework of embedded atomic potential model (EAM). By calculating the average energy, the pair distribution function (PDF), pair analysis for these particles and atomic packing, the following results are obtained. The structural changes of the nano-alloy particles originate from the position changes in the surface atoms, and the changes occur in a wide temperature range. As the particle size increases, melting temperatures of these particles approaches to the melting point of alloy bulk. For the small size particles, the arrangements in the surface atoms have large influence on the melting point. During the process of heating, the shapes of these nanoparticles change from quasi-sphere to irregular polyhedron. In the two nano-alloy particles’ system, the two particles are merged at room temperature, and there is a connecting region between them. Some defects such as atomic row misplacement exists in this region, and there is a tilting angle between the two particles. With the increase of the temperature, the connection region becomes wide or lengthen accompanying with the movements of the atoms. Below the melting point, there exists sliding of the two particles as the temperature increases. The particle size, space between the particles, and contacted facets affect the atom packing in the connection regions.