A street canyon is a typical urban configuration with surrounding buildings along the street, where emissions from vehicles are normally released. Buildings are the artificial obstacles to the urban atmospheric flow and give rise to limited ventilation, especially for deep street canyons. This study implements a large-eddy simulation (LES) coupled with a reduced chemical scheme (the LES-chemistry model) to investigate the processing, dispersion and transport of reactive pollutants in a deep street canyon. Spatial variation of reactive pollutants are significant due to the existence of unsteady multiple vortices and pollutant concentrations exhibit significant contrasts within each vortex. In practical applications of using one-box model, the hypothesis of a well-mixed deep street canyon is shown to be inappropriate. A simplified two-box model (vertically segregated) is developed and evaluated against the LES-chemistry model to represent key photochemical processes with timescales similar to and smaller than the turbulent mixing timescale. The two-box model provides the capability of efficiently running a series of emission scenarios under a set of meteorological conditions. In addition, a box model with grid-averaged emissions of street canyons is compared with a two-box model considering each street canyon independently (horizontally segregated) to evaluate uncertainties when grid-averaged emissions are adopted in a grid-based urban air quality model. This study could potentially support traffic management, urban planning strategies and personal exposure assessment.