Deep convection is an important process in determining tropospheric distributions of many chemical species including aerosols. Deep convection is one of the major sinks of atmospheric aerosols, while at the same time it supplies a certain portion of aerosols in the upper troposphere. On the other hand, aerosols can also influence deep convection and thus tropospheric chemistry by: (a) serving as CCN or IN and then impacting on cloud development and associated aqueous and gaseous reactions; and (b) serving as platforms for heterogeneous reactions that change the removal rates of certain chemical species. The impact of deep convection on aerosol redistribution and tropospheric chemistry has been studied using a three-dimensional cloud-resolving model including integrated dynamics, multiple mode and moment cloud and aerosol microphysics, gaseous and aqueous chemistry, heterogeneous chemistry, and radiation. The model is initialized using observational data. Various simulation results including concentrations of chemical species and aerosols in different modes have been compared with available in-situ aircraft observations. A number of model runs with various different settings in physics and chemistry have been carried out. The results of this study suggest that the existence of the deep convective towers and their associated anvils can change the distribution of UV fluxes and hence significantly alter the gas phase production of most chemical species. On the other hand, the formation of large amounts of ice as opposed to liquid water particles in deep convective zone is shown to greatly change the efficiencies of gaseous and aqueous reactions and provide a platform for heterogeneous chemistry. The latter process is found to be particularly important to the upper tropospheric budget of NOy. We found that clear differences exist in the upper tropospheric concentrations of aerosols with different sizes undergoing scavenging by cloud and precipitation particles. These physics-chemistry interactions along with transport related redistribution of chemical species and aerosols, all induced by deep convection, introduce quite different features to tropospheric chemistry comparing with the no-cloud case, particularly in the upper and lower troposphere.