The MEMS design and modeling tools that have been developed typically rely on finite element models, or even more coarse-grained macro models. However, some of the next generation of MEMS devices will be so small that the finite element models are pushed to the atomic limit where they fail, and a new type of model becomes necessary. The aim of this research work is to provide a systematic method to perform molecular dynamics simulation or evaluation for adhesion of micro/nano-gear train during surface sliding friction in MEMS. In this paper, molecular dynamics simulations of adhesion problem in micro-gear train are proposed. Based on analysis of surface sliding friction and the transmitting characteristics of micro-gear train, a simplified model to simulate surface sliding between metals by MD is proposed because the surface property is a dominant factor for the performance of gear system. The simulation results show that adhesion tends to occur between two micro-gears after certain cycles and such adhesion accounts for the friction force and the temperature increase. The driving force also plays a significant role on adhesion of micro-gears. The simulation results are in consistence with the experimental results in the literature. The MD model presented in this paper meets a lot of the important requirements of the tribology design of micro-gears and other heterogeneous MEMS. It is meaningful to prolong the lifetime of micro-gear train by using the model to select proper parameters.