Abstract The cool-roof strategy is an effective way of mitigating severe urban heat islands, and its impacts on urban flow and air quality deserve in-depth investigations. This study examines the effects of cool roofs on turbulent coherent structures and ozone air quality in Seoul, South Korea using the Weather Research and Forecasting-Community Multiscale Air Quality (WRF-CMAQ) model with a 50 m horizontal grid spacing. Cool roofs decrease the daily average air temperature, planetary boundary layer (PBL) height, and wind speed in the urban area of Seoul by 0.80 °C, 230 m, and 0.17 m s−1, respectively. Due to the lowered air temperature by cool roofs, the sea breeze and convective structures weaken and eddies at the PBL top appear less frequently. Since high O3 concentration air flows into Seoul by the sea breeze, the weakened sea breeze decreases the daily average O3 concentration near the surface by 3.3 ppb. Air at lower level is transported upward across the PBL top by convective structures and eddies at the PBL top. The transported air at lower level has lower O3 concentration and higher concentrations of O3 precursors than air at upper level. Therefore, the weakened convective structures and less-frequent appearance of eddies at the PBL top by cool roofs weaken the upward transport of O3 precursors at lower level across the PBL top. As a result, the chemical production of O3 and O3 concentration slightly above the PBL top are decreased. An integrated process rate analysis shows that cool roofs weaken the effects of turbulent coherent structures on O3 concentration.