Abstract: During the atmospheric reentry of reusable launch vehicles, the thermal protection system undergoes high-temperature ablation, leading to the formation of surface roughness. Simultaneously, the flow exhibits complex thermochemical nonequilibrium phenomena, such as internal energy excitation and chemical reactions at the molecular level. Under hypersonic conditions, the local flow gradients induced by these roughness elements significantly complicate the evolution of disturbances within the boundary layer, posing challenges for transition prediction. This study investigates hypersonic flat-plate flow using the Direct Simulation Monte Carlo (DSMC) method to perform unsteady, high-fidelity numerical simulations of boundary layers containing local roughness elements. By introducing specific-frequency disturbances into the freestream, the evolution of disturbance structures in the roughness wake is characterized. Furthermore, by comparing numerical results from real gas and calorically perfect gas models, the impact of high-temperature nonequilibrium effects on boundary layer characteristics is analyzed. The results indicate that when the characteristic size of the roughness element is large relative to the boundary layer thickness, it triggers flow separation and generates new compression and expansion waves, thereby intensifying thermal nonequilibrium effects. Additionally, the development of downstream disturbance waves is influenced by the upstream thermodynamic state and the geometric parameters of the roughness elements. This research elucidates the physical mechanisms of boundary layer disturbance response induced by roughness, providing valuable insights for the aerodynamic and TPS design of next-generation reusable spacecraft.