This work proposes a multi-scale simulation method that can simulate filling during the micro-injection molding process. The multi-scale simulation is comprised of two steps. In the first step, the macro-scale flow is analyzed using the conventional method. In the second step, the micro-scale simulation is conducted taking the slip and surface tension into consideration to investigate the filling of micro-cavity. Moreover, a conservative level set method is employed to accurately track the flow front. First, numerical tests have been done for circular micro-channels. The results show that slip and surface tension play important roles in the micro-regime. Second, to verify the multi-scale method, filling of a thin plate with micro-channel patterns has been simulated. The results show that the proposed multi-scale method is promising for micro-injection molding simulations.