The flow in natural river is mostly unsteady flow. Researching the local scour characteristics of step-shaped spur dike, a common waterway regulation structure, under the action of unsteady flow is of great significance to spur dike structure design and protection against flood damage. In the present research, the local scour characteristics of step-shaped spur dike under unsteady flow were discussed by establishing a 2-D mathematical model of flow and sediment. The natural inflow process was simplified as trough and peak inflow processes by using autoregressive Markov model. Research results demonstrated that the flow velocity in the main flow area and the recirculation area behind the spur dike changed with the upstream flow regardless of different discharge processes. The main flow area in trough inflow process gradually divided into two regions along with time, while in peak inflow process into two regions in the early stage. Influenced by the change of the main flow area and the siltation area behind the scour pit, the downstream boundary of the scour pit protruded towards the downstream and then retracted in trough inflow process, while in peak inflow process, the boundary of the scour pit shrank into the pit and then diffused to the downstream. The maximum scour depth at dam head can increase by 25.5%-54.3% compared with that in constant flow condition. L_d1, the length of the first-step spur dike, was used to characterize the scour pit scale; during the 6-hour scouring, the maximum length and width of the scour pit can reach 9.2L_d1 and 2L_d1 respectively in trough inflow process, and 11.3L_d1 and 2.1L_d1 respectively in peak inflow process.