Weather and climate models must simplify or approximate complex physical, chemical, and biological processes that occur in the real world, which gives rise to structural uncertainties. One case in point is the complex 3-D urban environment, which is often approximated by a 2-D urban canyon (called urban canopy models) in weather and climate models. Although these urban canopy models are widely used to study how the simulated urban climates respond to various perturbations/forcings (including but is not limited to anthropogenic heat emission), the structural uncertainty is rarely examined in these contexts. In this study, we aim to fill this research gap, focusing on the sensitivity of urban canopy air temperature to anthropogenic heat emission simulated by Weather Research and Forecasting-Single Layer Urban Canopy Model (WRF-SLUCM). We found that the sensitivity of urban canopy air temperature to anthropogenic heat flux can differ by an order of magnitude depending on how anthropogenic heat flux is released to the urban environment. Moreover, varying model structures through changing the treatment of roof-air interaction and the parameterization of convective heat transfer between the canopy air and the atmosphere can affect the sensitivity of urban canopy air temperature by a factor of 4. The substantial structural uncertainty highlights the challenges associated with simplifying complex urban environments in numerical models and calls for more research in this understudied area. Our study recommends using temperature sensitivity instead of temperature response to understand how various physical processes (and their representations in numerical models) modulate the simulated effects of anthropogenic heat flux.