With micro-plastic-mechanics theory and FEM（ finite element method）,the performance of a pair of micro gears mechanism is studied.The elastic-plastic finite element computation format based on the size effect is established and put into effect with UPFs（ User-programmable features） in ANSYS.This computation format is verified through comparing the micro-indention experiment of the polycrystalline copper with the computation results with FEM.Considering the size effect of the micro asperity,the influence of the micro geometric features（ burrs and roughness） in the manufacturing errors of gears on the performance of this mechanism is studied with substructure FEM with computation program.The basis is supported for the mechanical trace failure analysis of gear mechanism through the study and the computation efficiency and the accuracy of the simulation is improved.