One of the biggest uncertainties in numerical weather predictions (NWPs) comes from treating the subgrid-scale physical processes. For more accurate regional weather and climate prediction by improving physics parameterizations, it is important to optimize a combination of physics schemes and unknown parameters in NWP models. We have developed an interface system between a micro-genetic algorithm (μ-GA) and the WRF model for the combinatorial optimization of cumulus (CU), microphysics (MP), and planetary boundary layer (PBL) schemes in terms of quantitative precipitation forecast for heavy rainfall events in Korea. The μ-GA successfully improved simulated precipitation despite the nonlinear relationship among the physics schemes. During the evolution process, MP schemes control grid-resolving-scale precipitation, while CU and PBL schemes determine subgrid-scale precipitation. This study demonstrates that the combinatorial optimization of physics schemes in the WRF model is one possible solution to enhance the forecast skill of precipitation.