Air pollutants emitted within high-density urbanized areas have negative impacts on human health and quality of life and raise public concern. With the aim of creating a liveable environment and mitigating potential environmental problems, environmental scientists, architects and town planners have been working together to discover optimum building layouts and guidance principles for building morphology. These efforts have been consolidated via model simulations. Targeting an optimal design strategy, an improved SST k−ω model was first validated against wind and pollutant concentration data from a wind tunnel experiment at Tokyo Polytechnic University. The turbulence model was then applied to a variety of idealized city morphologies with different building permeabilities and building-height profiles. To confirm the findings from these idealized cases, further simulations were performed on two real conceptual cities. To facilitate pollutant dispersion within urbanized areas, at least 20% of the building permeability should be maintained, together with variations in building-height profiles. The innovative “Dragon Hole” design was also found to aid in pollutant dispersion. The study findings show that the pollutant concentration within the source canyon would be reduced by at least 40% for the idealized cases and by approximately 80% for the conceptual real case through incorporation of the abovementioned design features. Moreover, the recommendations resulting from this research are consistent with the requirements documented in the Sustainable Building Design Guidelines. •An improved SST k−ω model is applied to predict urban wind and pollutant fields.•Highly permeable building designs enhance pollutant dispersion within urban areas.•Pollutant transport would be enhanced under morphologies with height variations.•More than 20% building permeability is effective in limiting pollutant accumulation.•The combination of merit building design measures reduces pollutant trapping up to 80%.