In order to further understand the formation process of urban waterlogging and surface submergence under heavy rainfall, taking Xi’an New District as the research background, we established a Mike FLOOD coupling model of urban floods with the setting of different proportional green areas. With this model, the mitigation effect of green area on the accumulation of surface water and waterlogging risk under different scenarios were compared. The results show that with the increase of the proportion of urban green area, the submerged areas under the rainfall of 3 a, 5 a, 10 a and 20 a have been effectively controlled, especially when the proportion of green area is 35%. The submerged area with the water depth of more than 5 cm reduced by 20.64%, 20.83%, 18.42% and 18.40% respectively, and the decrease rate of the submerged area with the water accumulation time of more than 20 min was 31.18%, 24.40%, 24.55% and 23.33% respectively. Furthermore, the percentage of submerged area at the risk of waterlogging decreased by 30.26%, 23.98%, 23.25% and 23.07% respectively. However, the mitigation effect will be weakened with the increase of rainfall recurrence interval.