The simulation ability of tropical precipitation and convective vertical structure was evaluated using the two version of GAMIL (Grid-point Atmospheric Model of IAP LASG). In this work, we focused on the differences between GAMIL2 (G2) and GAMIL3 (G3), and the reasons for improved precipitation simulation in the G3 and the relationship between the convective vertical structure of tropical convection and precipitation simulation deviations were investigated. Both GAMIL versions accurately represent the key features of tropical precipitation, with G3 being more globally accurate than G2. The updated version greatly reduces the positive precipitation bias in the tropical Northwest Pacific Ocean. The water vapor budget diagnosis reveals that the precipitation deviation is primarily caused by the evaporation and the vertical advection dynamic terms, where the latter is attributed to the combined influence of vertical motion intensity and profiles. The vertical structure deviation of convection is most prevalent in the equatorial Indian Ocean and Atlantic Ocean areas, which primarily corresponds to small convergence component in the lower atmosphere and a larger height of detrainment. The traditional “top-heavy” and “bottom-heavy” vertical motion profile characteristics are strongly represented in the tropical northwest Pacific and equatorial Eastern Pacific Ocean, although deeper convection than reanalysis data is still evident. The moist static energy budget reveals that the estimated vertical motion divergence is primarily caused by the excess net energy flow across the tropical northwest Pacific Ocean. Alternatively, the deeper vertical convective structure leads to a larger gross moist stability, which offsets the net energy flux deviation and inhibits the convection in G3. This offset effect has significantly improved precipitation simulation in the tropical Northwest Pacific Ocean due to a decrease in the positive deviation of convective intensity. The down-regulation of convective stratus thresholds in G3 increases the frequency of convection and inhibits excessive vertical motion intensity. The vertical structure of tropical convection has various intimate links with precipitation deviation, which should be considered for future model development.