The Grid-point Atmospheric Model of IAP LASG version 2 (GAMIL2) has been developed through upgrading the deep convection parameterization, cumulus cloud fraction and two-moment cloud microphysical scheme, as well as changing some of the large uncertain parameters. In this paper, its performance is evaluated, and the results suggest that there are some significant improvements in GAMIL2 compared to the previous version GAMIL1, for example, the components of the energy budget at the top of atmosphere (TOA) and surface; the geographic distribution of shortwave cloud radiative forcing (SWCF); the ratio of stratiform versus total rainfall; the response of atmospheric circulation to the tropical ocean; and the eastward propagation and spatiotemporal structures of the Madden Julian Oscillation (MJO). Furthermore, the indirect aerosols effect (IAE) is −0.94 W m−2, within the range of 0 to −2 W m−2 given by the IPCC 4th Assessment Report (2007). The influence of uncertain parameters on the MJO and radiation fluxes is also discussed.