Navigation flow condition is one of the most important problems which should be considered in designing the shiplock intermediate channel. As the Dahua shiplock aqueduct is the intermediate channel of the former designed ship lift, it is different from the normal shiplock intermediate channel. Besides, the working head of the Dahua shiplock reaches 29.0 m, which makes the aqueduct hydraulic characteristics and flow regime become more complicated and severe, which can produce a serious influence on the ship safety and shiplock efficiency. Based on the classical theory of the open channel hydraulics, the basic hydraulic characteristics and the main factors affecting the flow conditions in the aqueduct are analyzed, and the comprehensive measures are adopted to improve the flow regime, including “soft measure” as the main and “hard measure” as the supplementary via model experiments and prototype observation. The “soft measure” means optimizing the valve schedule and the “hard measure” means setting up a wall at the end of the sloping section of the aqueduct. The measures have perfectly solved the complicated hydraulic problems and their validity has been testified by engineering practice.