In micro injection molding process, it is important to make each cavity filling uniform. However, there are many factors that cause cavity filling deviation like mold temperature differential between each runner, diameter differential of gates or runners by mold manufacturing errors. In this study, we do numerical analysis for locating major factors cause cavity filling deviation and suggesting more robust design for micro injection molding. We used thermal characteristic values of EP-7000, one of polycarbonate series polymers used for injection molding. And the widely accepted Cross-Arrhenius model is adopted for the viscosity of polymer material. For characterizing specific heat (Cp) and thermal conductivity (k), we used piecewise-linear method. And volume of fluid method and piecewise-linear interface scheme was used for visualization of polymer flow. 6 runners were modeled and we simulated four cases (mold temperature, runner’s diameter, gate’s thickness and complex condition of mold temperature and runner’s diameter). Numerical analysis has shown that case of mold temperature shows up to 28% difference in instant cavity filling rate and complex condition shows up to 33% difference. We suggest convergent runner and resin reservoir for reducing deviation. As a result, convergent runner design can reduce instant cavity filling rate deviation 20%, and resin reservoir design can reduce it 18%. Complex design of those two can reduce the deviation up to 22%.