Although high-speed vehicles are designed to be smooth, they tend to have some protuberances on their surfaces. Thus the aerodynamic characteristics and thermal loads are changed. Meanwhile, mounting protuberances on a flat plate is an important way of flow control, and appropriate structure and location of the protuberance can improve the performance of the scramjet inlet remarkably. The nanotracer planar laser scattering (NPLS) technique is used to test the flow field of Mach 3.0 supersonic flow over circular protuberances of different heights. In total three models are tested. And the second-order scheme and fifth-order weighted compact nonlinear scheme (WCNS-E-5) is adopted to simulate the flow field. Fine structures of supersonic flow over the circular protubernaces have been obtained and the development of boundary layer in the wake flow can be observed. By comparison, it may be concluded that the protuberance lower than the local thickness will have weak disburances on its boundary layer development, and the layer after reattachment can keep its laminar state within a long distance. During the transition many clear hairpin vortices can be distinguished. When the protuberance height is larger than the thickness of the boundary layer, and the later in the region of wake flow would develop into a turbulence quickly due to intense disturbances. The transition point observed from the experimental results lies closer to the protuberance, and this might be cansed by the noise from the walls of the wind tunnel. Intermittency analysis has been done for the boundary layer in the wake flow based on the NPLS images, and the results show that the intermittency curves of the two protuberances that are larger than the local boundary layer thickness are quite similar and fluctuations are strong.