GRAPES and MM5 models are used to simulate and predict the heavy rainfall process in Chongqing in September 2004. The result shows that both models can predict the rainfall development successfully, but there are certain differences between observation and simulated center location and magnitude of rainfall. The rainfall spatial distribution simulated by GRAPES is better than that simulated by MM5. However, the maximum values of the precipitation center are much less than the results of MM5. It is noted that the vertical velocity simulated by MM5 is higher than that simulated by GRAPES through analysis of the general circulation, which may cause the difference in the rainfall magnitude. Through the preliminary diagnostic analysis of simulation, it can be found that the simulation for conditional instability has impact on the spatial distribution prediction for both models.