The navigable clearance scale is a key factor to be considered in the selection of bridge type schemes on urban navigable rivers, especially in the case of limited clearance, the restriction of pier size and shape on navigation is obvious. In this paper, the impact of different pier structures on navigable flow is analyzed through the two-dimensional flow mathematical model test of new bridge section of a river. The results show that the shape optimization of square pier chamfer can reduce the transverse velocity of navigable waters; and the larger size of pier, the greater transverse velocity of navigable waters. Furthermore, the transverse velocity of the navigable waters is the smallest on the condition of the same width but round form of head pier structure. The test data can effectively solve the contradiction between bridge navigation and landscape construction on urban navigable river, and provide a variety of options for bridge construction.