Abstract: Transition from laminar to turbulent flow of the hypersonic boundary layer can increase the wall friction coefficient and heat conduction coefficient by 3 ~ 5 times, which has a significant influence on flight performance and safety of hypersonic vehicles. Wavy roughness is a possible passive control method to delay hypersonic boundary layer transition, and is thus of engineering significance. In this paper we investigate the effort of finite-length wavy roughnesses with different locations and heights on the stability of a Mach 6.5 flat-plate boundary layer using direct numerical simulation and linear stability theory (LST). DNS is employed to obtain the laminar base flow, and to study the linear evolution of fixed-frequency disturbances parametrically introduced upstream by blowing and suction. The effects of the relative position of the fast/slow mode synchronization point and the wavy roughness are revealed. It is found that when the wavy roughness is placed upstream of a disturbance’s synchronization point, the disturbance is damped compared to the smooth surface case; when the disturbance’s synchronization point is within or slightly downstream of the wavy roughness, the disturbance is generally enhanced. The effects of heights of wavy roughnesses are also considered. For the wavy roughness with small heights compared to the boundary layer thickness, the effect of wavy roughness is positively correlated with the height of the wavy roughness, while the effect is weakened by the higher wavy roughness. Linear stability theory can predict well the effects of wavy roughness on high-frequency disturbances, but exhibits large discrepancies with DNS in predicting the behaviors of moderate and low-frequency disturbances. This indicates that the receptivity process and the strong non-parallel effect in the vicinity of the wavy roughness neglected by LST should play an important role.