By changing the alignment angle of spur dike, this study focused on the evolution of scour hole morphology in three alignments under clear-water scour conditions, including the 3-D structure of the scour hole, 2-D profile morphological evolution process and the evolution characteristics of the local bed shear stress. The results show that the plane area and volume of the scour hole both are power functions over time, which is similar to the evolution characteristics of scour depth. Local scour includes three stages: The initial stage, development stage and balance stage. The local bed shear stress presents successively: τb > τc, τb = τc and τb < τc. Based on this characteristic, the evolution mechanism between scour hole morphology and the local bed shear stress is further clarified. Furthermore, although the alignment of the spur dike significantly affects the longitudinal and vertical dimension erosion rates of the scour hole, the scour hole morphology is not only relatively constant but also has a specific proportion, and the evolution process is orderly in the whole process of evolution. To the scouring equilibrium state, the length of the scour hole on the upstream and downstream of the spur dike is approximately in line with the golden section feature. The related results provide technical support for scour parameter design and scour hole protection of spur dike in flood period.