To scientifically guide the prevention transformation project of drainage and waterlogging in urban overpass and reduce the risk of waterlogging, a high-resolution urban waterlogging model has been constructed using an overpass in Shenzhen as the research object, and the model was calibrated and verified by using measured surface water data to simulate flow accumulation in the overpass tunnel under different design rainfall before and after the reconstruction of the rainwater outlet anti-blocking, the sunken greenbelt, and a joint measure of these two infrastructures. The results show that 1) the high-resolution urban waterlogging model can accurately simulate the dynamic change process of flow accumulation in urban overpass. 2) Under 5-year, 20-year, and 100-year return period of rainfall, the overpass tunnel displays serious waterlogging, while the temporal and spatial change rate of flow accumulation is rapid. Under the 100-year return period of rainfall, the maximum accumulated inundation depth and area are as high as 1.52 m and 1833 m², respectively. The maximum growth rate of inundation depth over time and space are as high as 0.04 m/min and 0.23 m/10 m, respectively. 3) The waterlogging reduction of combined measure is more efficient than that of various renovation measures used separately. Under the rainfall of 100-year return period, there is still ponding with a depth of over 0.6 m when the measures of rainwater outlet anti-blocking or sunken greenbelt are taken alone. With combined measures, the inundation depth could be lower than 0.5 m, and the waterlogging duration could be shortened to less than 30 min, which can effectively alleviate the waterlogging of overpass tunnels.