Polymethyl Methacrylate (PMMA) nanochannels are becoming increasingly important for biological, optical and electronic applications. To form a complete PMMA nanochannel/device, the open nanotrench will always be thermal bonded. However, the bonding process which influences the final fabrication precision of PMMA devices has not yet been studied systematically by numerical simulation. In this work, an elastic–plastic model was used for PMMA nanochannel bonding. The influence of temperature, pressure, aspect ratio, and friction coefficient on the dimension loss and max stress was studied systematically. By numerical simulation, all the main influence factors were optimized. It is expected that the proposed simulation method has a high potential for the polymer bonding process analysis.