To study the impacts of urban underlying surface characteristics on thunderstorms in Nanjing, a mesoscale numerical model is used to study a specific case occurring on July 23, 2011. The Weather Research and Forecasting (WRF) model, coupled with the Noah/Urban Canopy Model (UCM), used 1°×1° four times daily global analysis data from the National Centers for Environmental Prediction Global Forecast System (NCEP FNL) and observation data from the Nanjing automatic weather stations. The simulated results suggest that the occurrence and the development process of the thunderstorm are closely related to urban underlying surface in this region. In particular, the urban heat island effect in Nanjing is evident before the thunderstorm. Moreover, the sensible heat flux over the urban region is significantly higher than that over the surrounding regions. This, combined with the effect of the urban heat island circulation, caused surface thermal differences between urban and rural areas, which enhanced the convergence over the urban areas and provided the uplift for the formation of the thunderstorm. The expansion of the urban underlying surface is attributed to a larger boundary layer thickness and vertical mixing height, which contributed to cloud development. In addition, the perturbations in the potential temperature of the lower atmosphere were also enhanced by the urban underlying surfaces, offering unstable stratification conditions for the thunderstorm. Finally, larger roughness over the urban underlying surface caused precipitation of the thunderstorm in the windward side of the city of the low-level surface to increase significantly.