As a convenient way for the assembly of thermal plastic MEMS (Micro Electro-Mechanical Systems) devices fusion bonding was studied in molecular level. The diffusion behavior of polymer molecular chains was simulated by molecular dynamics. Amorphous PMMA (poly methyl methacrylate) layer were constructed. The interaction of PMMA layers in heating and cooling stages were simulated in NPT ensemble. In the simulation the PMMA molecular chains spread across the interface and entangled with the chains in the other layers. The factors including pressure and temperature which play important role in fusion bonding were analyzed in molecular level. System deformation was recorded in heating and cooling progress. Diffusion depth and binding energy in the model which had experienced heating and cooling simulation were obtained to investigate fusion degree. Deformation and fusion degree increase with larger pressure and higher temperature imposed to the system. It is concluded that only considering the diffusion of molecular chains parameters of relatively small pressure and high temperature are necessary to obtain precise bonding for micro joint, which is significant in guiding the precise bonding for micro assembly.