To investigate the model simulation accuracy of secondary flow and eddy structure in dynamic bed bends, the simulation accuracy of bed morphology during scouring and siltation process in bends by the large eddy model (LES) and the RNG k-ε model was verified by the scour flume experiments of a 90° horizontal bend by Barbhuiya, and the results of the LES model were found to be more accurate. Based on the simulation results of the LES model, the bottom vortex structure generated by secondary flow was identified by the Q criterion, according to which the quantitative effect of vortex structure on bed scouring and siltation was analyzed. The results show that in the process of clear water scouring the dynamic bed bend, the bottom vortex tends to be stable when the Q value is between 30-50, and becomes strong enough to affect the bed scouring and siltation when Q>50, because a strong and stable vortex structure can stabilize the bed morphology, leading to a constant bed scouring and siltation rate, which changes within 2×10-6 m/s. According to the analysis of the relationship between the shear flow velocity in the bend and the bed morphology, there are two types of high shear flow velocity areas in the bend, when the shear velocity value of the first type area is larger than that of the second type, obvious scouring pits with a depth greater than 0.10 m will appear on the bed surface. The results of this study can be used as a reference for the simulation of siltation equilibrium and bed morphology in the bends.