[Objective] Water intake structures of reservoir connection projects are characterized by large water level fluctuations, bidirectional flow, and operating modes affected by pipeline roughness, leading to a relatively complex hydraulic regulation process. Poor intake design or unreasonable regulation can easily cause a series of problems. To analyze the key hydraulic issues of water intake structures in reservoir connection projects, this study took the Gongming-Qinglinjing Reservoir Connection Project as the research object. The hydraulic characteristics of bidirectional water intake and layered control intake were systematically investigated, and key issues and corresponding measures that needed to be focused on in the design of various types of water intakes were proposed. [Methods] Firstly, the hydraulic calculation method was used to analyze the hydraulic characteristics of the main conveyance line under different operating conditions and to assess the impact of roughness variation on flow conveyance capacity and water intake operating conditions. On this basis, hydraulic model tests were conducted to examine the flow patterns and local hydraulic characteristics of the bidirectional water intake and layered control intake under typical scheduling conditions. Finally, regarding the transitions between free surface and pressurized flow as well as closed hydraulic jump in the connecting tunnel behind the gate of the layered control intake, optimization recommendations were proposed from the perspectives of engineering measures and operational scheduling. [Results] (1) the selection of roughness had an important impact on the project’s water conveyance capacity, water intake hydraulic characteristics, and project hydraulic scheduling. When the roughness increased from 0.011 to 0.016, the pipeline head loss increased by 108.2%-111.6%. Under maximum roughness conditions, the water conveyance capacity of the project must be ensured, while under small roughness conditions, particular attention must be given to the flow connection characteristics at the water intake. (2) Under inflow conditions, at bidirectional water intakes, the water surface in the reservoir area and the diversion channel was stable, the flow velocity was relatively small. After entering the intake tower, the flow velocity increased, with no adverse flow patterns such as vortices or recirculation. Under outflow conditions, the flow at the water intake was smooth. The main flow increased in velocity after entering the diversion channel from the forebay, generating symmetrical recirculation on both sides. (3) During gate-controlled discharge, the layered control intake exhibited a free jet flow pattern. The jet impacted the wall of the energy dissipation well, fell to the bottom, and then entered the connecting tunnel section in an open-channel flow state. Adverse flow patterns such as closed hydraulic jumps might occur in the connecting tunnel. (4) Regarding the issue of closed hydraulic jumps, feasible preventive measures were proposed from the perspectives of engineering solutions and operational scheduling. (5) Reservoir connection projects had complex operating conditions. After the project was commissioned, the actual roughness of the main tunnel should be inversely calculated based on monitoring data, and the hydraulic control methods should be adjusted in a timely manner. The research findings can provide references for the design and operational scheduling of water intakes in similar water diversion projects.