In this research, a molecular dynamics simulation model of thermoplastic nanoimprint lithography process is proposed. The model is imprinting a gold mould into a PEO film to study the polymer deformation behavior. The polymer deformation is observed in the thermoplastic nanoimprint lithography process by using five different aspect ratio moulds with two different cooling down temperatures. The distribution of stress and density in the systems is investigated to discuss the effect of the systems with different aspect ration moulds. The interacting forces are obtained by dividing the polymer into three regions between the polymer and the mould. Discuss about the friction effect in the systems. Finally, redesign a new mould trying to improve the phenomenon that the large stress couldn’t release completely in old nanoimprint process.