The impact of tropical deep convection on tropospheric chemistry has been studied using a three-dimensional cloud-resolving model including integrated dynamics, cloud and aerosol microphysics, gaseous and aqueous chemistry, heterogeneous chemistry, radiation, and parameterized lightning production of NO. Initialized with observational data over the tropical oceans, a number of model runs with a 500 by 400 by 25 km domain and 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. Under this kind of circumstances, NOx molecules produced by lightning are found to collectively change the main tropospheric chemical pathways and significantly influence the budgets of many chemically important species and thus the ozone related chemistry. 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 trpospheric budget of NOy. These physics-chemistry interactions along with transport related redistribution of chemical species, 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. The results of this study also suggest the importance to consider the impact of chemistry and physics-chemistry interaction, not just vertical transport, on the redistribution of chemical species when parameterizing convection in large-scale model.