Based on TELEMAC-2D model, a flood simulation model of the Shenzhen River Basin in Shenzhen City was established. Two measured rainstorm events (20180607 and 20180916) were selected for model verification. The results show that the established model has good reliability and accuracy. The established model was used to simulate the process of flood and waterlogging under the conditions that the return period of rainstorm is 50 years, the rainfall peak coefficient is 0.4, and the rainfall duration is 30.min, 60.min, 90.min and 120.min, respectively, to obtain the disaster causing factors such as the ponding depth, ponding area and flow velocity. Considering the combination of different flow velocity and ponding depth, the risk assessment of waterlogging in the Shenzhen River Basin was carried out. The results show that with the increase of rainfall duration, the ponding depth, ponding area and flow velocity increase. According to the ponding depth and flow velocity, the flood risk zoning of the Shenzhen River Basin is carried out. The areas of medium- and high-risk zone increase with the increase of rainfall duration. Medium- and high-risk zone areas account for a small proportion of the total area of the basin, but are prone to casualties and property losses. When medium and high-risk zone occur, information shall be released in time and emergency and disaster reduction measures shall be actively taken.