Abstract: During the atmospheric reentry of reusable launch vehicles, the thermal protection system undergoes high-temperature ablation, leading to the formation of surface roughness. Concurrently, the flow exhibits complex thermochemical nonequilibrium phenomena, including internal energy excitation and molecular-level chemical reactions. Under hypersonic conditions, the local flow gradients induced by such roughness elements significantly complicate the evolution of disturbances within the boundary layer, posing challenges for transition prediction. In this study, the direct simulation Monte Carlo (DSMC) method is employed to perform unsteady, high-fidelity numerical simulations of hypersonic boundary-layer flows over a flat plate containing local roughness elements. By introducing specific-frequency disturbances into the freestream, the evolution of disturbance structures in the roughness wake is characterized. Furthermore, the impact of high-temperature nonequilibrium effects on boundary-layer flow characteristics is analyzed through a comparison of numerical results obtained from real-gas and calorically perfect gas models. The results indicate that when the characteristic size of a roughness element is large relative to the boundary-layer thickness, flow separation is induced, accompanied by the formation of new compression and expansion waves, which significantly amplify thermal nonequilibrium effects. Under perturbed freestream conditions, both the upstream thermodynamic state and the geometric parameters (size and location) of the roughness elements considerably influence the development of downstream disturbance waves. A systematic analysis of 25 test cases reveals that optimal disturbance suppression is achieved when the roughness element is positioned at x = 0.0125 m with a relative height H = 0.5δ, yielding a 72% increase in the disturbance attenuation rate compared to a smooth flat plate. As the roughness height increases, the suppression effect exhibits a non-monotonic trend, initially weakening and then strengthening, whereas as the roughness element moves downstream, the suppression effect first strengthens and then weakens. Moreover, three-dimensional roughness elements induce additional spanwise disturbance components and enhance wake mixing. This modulating effect on disturbance evolution cannot be neglected. This study elucidates the physical mechanisms underlying the boundary-layer disturbance response induced by roughness elements under hypersonic conditions, providing valuable insights for the aerodynamic and thermal protection system design of next-generation reusable spacecraft.