Abstract: Partition dikes between sluices and locks of hydropower projects are an effective measure to improve navigable flow conditions. Traditional partition dikes adopt impermeable or dike-opening structures. The upgrading of locks and the increasing complexity of operating conditions lead to difficulties in meeting specifications for navigable flow conditions in the approach channel and entrance area. Permeable partition dikes, such as bottom-permeable structures and diversion piers, have therefore come into use. However, it is still often necessary to reduce the maximum navigable discharge to ensure navigation safety. To meet the conditions required for safe vessel maneuvering within the approach channel, separation dikes of sufficient length should be arranged between the ship lock and structures such as overflow dams, sluice gates, and power stations. It is recommended that when the longitudinal flow velocity exceeds 0.5 m/s, the length of the separation dike on the outer side of the approach channel should extend to cover the area beyond the braking section. The proposed Huai’an East Ship Lock is an important component of the supporting navigation project for the second phase of the Huaihe River Seaward Waterway. A comprehensive physical model with a geometric scale of 1:90 was established to conduct experimental research on downstream navigable flow conditions, and the downstream separation dike was optimized accordingly. The structure adopts a pile-cap and pier–slab configuration. Optimization tests focus on the length of the pier–slab separation dike, the type of bottom openings, and the opening height. If a fully enclosed separation dike is adopted, the flow regime in the approach channel and entrance area becomes relatively disordered, manifested as large-scale crossflow and backflow in the entrance area. Downstream of the Huai’an East Ship Lock, the measure of extending the separation dike to cover two-thirds of the braking section has been implemented. The total length reaches 360 m, with the lower 320 m gradually transitioning to a permeable structure from bottom to top. The porosity ranges from 25% to 8%, with an average porosity of 15%. It can effectively eliminate the backflow in the entrance area. A weak backflow exists within the approach channel, with the maximum crossflow traversing the channel reaching 0.15 m/s. Based on the existing physical model, comparative tests were conducted under the same flow conditions for five structural types: fully enclosed baffle plates, bottom-section gradual porosity, uniform porosity at a consistent bottom height, and full-section uniform porosity. A new type of full-section uniformly permeable structure is proposed, and the improvement effect is investigated by physical model tests. The results indicate that the new structure of permeable partition dike can make the mainstream and the flow in the approach channel mix gradually and evenly, effectively improve the flow regime in the approach channel and the entrance area, and reduce the intensity and range of crossflow and backflow. Under this scheme, the maximum crossflow generated by the backflow within the approach channel is only 0.10 m/s, with a backflow length of 230 m—exceeding one time the length of the designed single vessel. This has relatively minor impact on navigation safety and significantly improves the flow regime. If the separation dike serves solely as a flow-dividing structure, a uniformly permeable structure across the entire cross-section can be adopted. Its placement should avoid the design highest navigable water level and the normal water level to the extent possible. Under the same conditions, it significantly increases the maximum navigable flow of the ship lock, ensures the number of navigable days and navigation safety, and provides a new method for the design of diversion channel separation dikes under complex boundary conditions.