Urbanization has promoted economic growth but it can increase gust wind speed, which may lead to serious damage to infrastructures. This study uses the Weather Research and Forecasting model and a gust parametrization scheme to evaluate the mitigation impact of white roofs and green roofs on wind gust over the Pearl River Delta, an urban agglomeration in Southern China in June, July, and August of 2014. The results show that both white and green roofs decrease the gust wind speed by decreasing the mean wind speed, suppressing the turbulent motion and weakening the convection. The impacts of white roofs are stronger than those of green roofs. The daily mean reductions of gust wind speed are approximately 1.2–1.3 m s−1 (12%–16%) and 0.4–0.6 m s−1 (6%–10%) by white and green roofs, respectively. In general, the contribution of turbulence (60%–85%) to the gust wind speed is the largest, and the contribution of mean wind speed is approximately 10%–30%, however, the effect of deep convection is not obvious (0%–15%) on the decrease of gust wind speed. The effect of cooling roofs on reducing the gust wind speed is stronger during daytime than during nighttime, and the effect is more significant in city areas that have higher building densities. Based on the findings, this study is potentially beneficial for policy-makings in developing urban disaster mitigation methods.