In order to ensure that the structure of the stormwater model is well aligned with the actual physical phenomena, thereby guaranteeing the accuracy of the stormwater simulation results in flood prevention planning, a set of methods for improving the accuracy of complex integrated embankment stormwater simulation is proposed. The drainage patterns of complex integrated embankment are analyzed, revealing the drainage characteristics of complex integrated embankment and the features of floodwater discharge within the internal areas of the integrated embankment. The runoff characteristics of different terrains in the areas and their suitable simulation methods are also examined. Based on these analyses, a method and steps for constructing a stormwater model for complex integrated embankment are proposed. Taking the Zhongshan-Zhuhai integrated embankment in the Guangdong-Hong Kong-Macao Greater Bay Area as an example, an empirical study on the construction of a complex integrated embankment stormwater model is conducted. The results show that the constructed model structure is consistent with the actual stormwater process, with high precision and stable performance in calibration and testing. The average Nash-Sutcliffe efficiency coefficient is 0.05 to 0.61 higher than that of other model structures that do not follow the drainage process of the integrated embankment.