Numerical simulation of roughness effect on modal growth is conducted on a hypersonic flat-plate at Mach 5.92. The steady base flow is firstly simulated by solving compressible Navier-Stokes equations. Stability characteristics of boundary-layer waves are analyzed by linear stability theory (LST). In stability simulations, two-dimensional disturbances corresponding to mode S or mode F at a frequency of 100 kHz are introduced near the leading edge of the flat-plate. Roughness with adjustable height is placed into four locations with respect to the disturbance synchronization point. It is found that upstream of synchronization point, disturbance is amplified by roughness with a stronger strength for taller roughness. On the other hand, disturbance is damped when the roughness is placed at or downstream of synchronization point. Different from upstream cases, tall roughness damps disturbance instead of amplifying it. We believe the relative location of synchronization point and roughness is a candidate to explain roughness delay transition as previous experiments have shown. Our results also show that roughness effect on mode S and mode F are very alike. In addition, a disturbance with a wide bandwidth is planned and will be imposed in the future.