The ablation of the thermal protection system (TPS) on the aircraft surface generates distributed roughness elements (DRE), which is expected to affect the hypersonic boundary-layer instability seriously. This work presents the experimental investigation of hypersonic boundary-layer instability waves on a 7° half-angle sharp cone with DRE allocated downstream of synchronization point at 0° angle of attack using surface flush-mounted pressure sensors, focused laser differential interferometer (FLDI), infrared thermography and schlieren technique. The experimental results showed that when the DRE (lower than the local boundary-layer height) was located downstream of the synchronization point, the Mack second mode still dominate the boundary-layer instability, and the transition onset was not significantly affected by DRE at various Reynolds numbers. Based on further analysis in the region downstream of roughness, the DRE didn't influence the nonlinear interaction among instability waves materially, although it promoted the growth of instability waves compared with the smooth case. However, the nonlinear interactions were decaying adjacent to the DRE, as the Mack second-mode instability waves cannot penetrate into the separation bubble because of the flow separation induced by the DRE. The FLDI measurement along the wall-normal direction revealed the second-mode instability waves were suppressed close to the wall by the complex roughness surface at the DRE region, and also confirmed the existence of second-mode instability waves at these streamwise locations. The evolution of instability waves followed the linear stability theory (LST), despite the existence of complex wall surfaces. This work enriches the understanding of the effect of DRE on hypersonic boundary-layer transition and demonstrates the spatial characteristics of instability waves above the complex surface.