Green roof and cool roof are two popular strategies to mitigate urban heat island especially in the summer time. The meteorological effect (cooling on the near surface temperature) of the two mitigation strategies has been proved by lots of studies while the environmental effect (effect on urban air quality) is still largely unknown. In this paper the WRF-Chem model coupled with a single layer urban canopy model is used to simulate three heat wave and heavy ozone pollution episodes in Shanghai, China. Sensitivity experiments of green roof and cool roof are carried out and the results show that both green roof and cool roof can effectively mitigate urban heat island, and their cooling efficiencies are similar even their cooling mechanisms are different. All of them can reduce the lasting time and area of high temperature and extreme hot, but the ozone pollution may become more serious. According to the different ambient wind field and ozone distribution, these three ozone pollution episodes can be divided into two conditions: urban dome and urban plume. The decrease of urban surface temperature can inhibit the turbulent activities and reduce the height of the boundary layer; the concentration of ozone in urban Zone A (below 750 m height) increases, but decreases in urban Zone B (750 m-2km height) for urban dome. By calculating the ozone fluxes at different heights, we find that the urban heat island circulation can transport surface ozone into city, horizontally; while in Zone B, the horizontal divergence transport ozone out of the city, and green roof and cool roof can decrease the temperature difference between urban and suburban, which can inhibit this ozone transportation of urban heat island circulation.