The second phase of the Huai’an Water Control Project needs to build an additional aqueduct，which may affect the navigation conditions after forming a long-distance navigation aqueduct with the first phase aqueduct. Aiming at the problem，a three-dimensional mathematical model is established，and the navigation conditions of the aqueduct before and after the construction of the second phase aqueduct are simulated and analyzed by selecting two operating conditions under the most unfavorable combination of ship types. They are the operating conditions of the upstream and downstream ships in the opposite direction，and the energy dissipating grid is arranged or not.Conclusions are drawn：1）The wave height after the completion of the second-stage aqueduct is increased by about 20% without the energy dissipating grid，and the wave height is reduced to 7% after the energy dissipating grid is added. 2）The cross flow is at 0.05~0.20 m/s，and the Froude number is far less than 1. The bow deflection angle is 0.64°~1.74°. They have little change from the current operating conditions. 3）The long aqueduct composed of the first and second phases has good navigation conditions and will not cause adverse effects on the navigation of the ship.