The variations of erosion or deposition of the riverbed caused by water and sediment movement are a common phenomenon in nature, which often causes practical engineering problems such as river sedimentation, river bed deformation, coastal retreat, reservoir capacity reduction. The results are closely related with the design, construction and operation of water projects. Therefore, it is of great significance to study the accurate and efficient methods of riverbed three dimensional terrains reconstruction and analyzing the volumes of erosion or deposition. In this paper, flume experiments with bed load sediment transport were conducted to study the river bed evolution under different flow conditions. Based on the Structure from Motion (SFM) method, three-dimensional terrain reconstructions of bed surface were carried out before and after scouring experiments to obtain the dense point clouds. On this basis, the same ground control points (GCPs) were fixed to acquire the actual three dimensional terrain coordinates, and then three dimensional point cloud coordinates were interpolated in the river bed mesh to accurately analyze erosional and depositional quantities of the whole bed. In this paper, the methods of SFM were introduced in details, containing the shooting method, selection of GCPs, the establishment of river-channel mesh and the interpolation method. The results show that: (1) the volumes with the presence or not of block model were calculated by SFM respectively to verify that the relative error of present method is less than 4%; (2) The variation qualities of erosion or deposition calculated by SFM method and the qualities of the actual weighing were comprised together to show that the relative error of present method is less than 5%; (3) This method was also applied to the large-scale river model experiment, and the relative error is less than 10%. The results above show that present method can be applied in both flume experiment and larger river bed physical model experiment, to reconstruct the three-dimensional bed topography quickly and efficiently. The paper offers an innovation idea and reference of researching the bed evolution and hydraulic model experiment.