The present study concerns the analysis of the numerical simulation of filling phase of a micro gear in the micro molding process. In this process, the non-isothermal molten polymer flow is injected from the gate of the cavity which initially occupied by the air, giving a two-phase flow. In this model, the Navier Stokes and energy equations were coupled with the level-set equations in order to track the melt polymer front evolution versus time. The molten polymer is considered as a generalized Newtonian fluid and his viscosity dependent of shear rate and temperature is modeled by the Cross-Arrhenius model. The effect of thermal contact resistance was investigated. The velocity, temperature, pressure, and viscosity field are calculated versus time and discussed.