The Linhuaigang flood control project (LFCP), situated on the Huaihe River, China, uses the river channels upstream of the LFCP, together with the hinterland areas outside the channels, to retain and store fluvial floodwaters that exceed the downstream channel’s discharge capacity. The hinterland areas are split into seven flood storage areas, three floodplain areas, eight polder areas, and three flood-control-protected areas, and they are connected to the river in various ways. A coupled hydrodynamic model was established to simulate the hydrodynamic and water volume exchange between the river channels and the hinterland areas. The flood storage area, under the control of a flood diversion sluice, was simulated with a 2D hydrodynamic model, and the inflow process initiated by the flood diversion sluice was simulated as a control structure. The polder area was generalized as a reservoir that would be filled in several hours once put into use because of its small size. The uncontrolled inflow process between the flood-control-protected areas and the channel was simulated by means of a dam break model, which could simulate levee breaching. The flooding within the flood-control-protected area, which represents a vast space, was simulated with a 2D hydrodynamic model. The floodplain area was laterally connected to the river channel along the river levee. The difference between the simulated and the measured flood peak water stage did not exceed 0.2 m in 2003 and 2007, indicating that the accuracy of the model was relatively high. In the scenario of a design flood with a return period of 100 years, the flood storage areas and the LFCP were used in the following order: Mengwa, Qiujiahu, Nanrunduan, Shouxihu, Jiangtanghu, Chengxihu, Chengdonghu, and the LFCP. When the Huaihe River encounters a flood with a return period of 1000 years that exceeds the design standard, the highest water stage upstream of the LFCP and Zhengyangguan shall not exceed 29.30 m and 27.96 m after the use of all the flood storage areas, floodplain areas, and flood-control-protected areas. The results of this research can provide technical support for the flood risk management of the LFCP.