The process of clear-water scour is very usual phenomena in natural river. So far, most of the previous studies mainly aim at the calculation of bed armoring layer and process of sediment transport with the action of the flow scour. However, there has been very little attention paid to the flow structure, in particular, the changes of flow structure among different armoring levels for the limitation of monitoring setups. The stable bedform and flow structure on the clear-water scour in gravel-bed flume have been measured by means of acoustic doppler velocimeter (Sontec ADV) and Nikon DTM. The results show there is a close relationship among flow, bedload transport, bed material and bedform. The distribution of coarse surface on the armoring layer was affected by the initial bed and its armoring degree with the closely experimental condition. The mean velocity profile may be changed from the logarithmic velocity distribution to the S-shaped curve along relative water depth direction because of the changes of impacted factors, in addition, there is a very good interrelationship between the maximum of turbulence kinetic energy (TKE) and the minimum of mean velocity, but the transitional region and detail location were strongly related to the experimental conditions of flow, sediment and bedform.