The design of water conveyance system is the key work of ship lock engineering design. The rationality of its design determines the effect of water conveyance and the durability of the ship lock. The size of water conveyance culvert directly affects the time of water conveyance and mooring condition. To determine the reasonable size of water conveyance culvert and structure section, this paper takes a junction lock as an example, from the perspective of the hydraulic structure and economic analysis, uses the finite element method to calculate the structure internal force of structure section corresponding to the sizes of two different water conveyance culverts, and makes a comparative analysis of the different structure section from engineering cost, and gets a better lock structure section with the reasonable size of the water conveyance culvert.