The new driving mode of hydraulic power is instead of electric power in the hydraulic ship lift，which is a milestone in the field of navigation of high dam. In order to ensure the safe operation of the hydraulic ship lift，the risk assessment is carried out for its water conveyance system. In this paper，a theoretical system of operation risk assessment method for water conveyance system of hydraulic ship lift is established. The operation principle of the water conveyance system is analyzed，and the risk characteristics of the water level not equivalence phenomenon in the shafts are expounded. Based on the cloud model theory，an early warning index of the water level not equivalence phenomenon in the shafts is established. By taking the Jinghong hydraulic ship lift as an example，the threshold of the risk index of water level not equivalence phenomenon in the shafts of water conveyance system in the 100-meters level of hydraulic ship lift is predicted. The results show that this method can effectively control the risk of the shafts water level not equivalence phenomenon，and can be applied to the risk early warning of hydraulic ship lift，and can be used to provide decision-making for the running risk prevention of hydraulic ship lift.